{"id":"https://openalex.org/W2016106183","doi":"https://doi.org/10.1002/prot.22397","title":"Crystal structure of the conserved hypothetical protein TTHA1606 from Thermus thermophilus HB8","display_name":"Crystal structure of the conserved hypothetical protein TTHA1606 from Thermus thermophilus HB8","publication_year":2009,"publication_date":"2009-02-02","ids":{"openalex":"https://openalex.org/W2016106183","doi":"https://doi.org/10.1002/prot.22397","mag":"2016106183","pmid":"https://pubmed.ncbi.nlm.nih.gov/19322824"},"language":"en","primary_location":{"id":"doi:10.1002/prot.22397","doi":"https://doi.org/10.1002/prot.22397","is_oa":true,"landing_page_url":"https://doi.org/10.1002/prot.22397","pdf_url":"https://onlinelibrary.wiley.com/doi/pdfdirect/10.1002/prot.22397","source":{"id":"https://openalex.org/S121161810","display_name":"Proteins Structure Function and Bioinformatics","issn_l":"0887-3585","issn":["0887-3585","1097-0134"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["cwts-core","dongbi-c","doyens","jufo-1","ki-jl-1","medline","norway-1","poland-100","russia-white-list-2"],"host_organization":"https://openalex.org/P4310320595","host_organization_name":"Wiley","host_organization_lineage":["https://openalex.org/P4310320595"],"host_organization_lineage_names":["Wiley"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proteins: Structure, Function, and Bioinformatics","raw_type":"journal-article"},"parent_works":[],"lineage":["https://openalex.org/W2016106183"],"child_works_count":0,"type":"article","is_traditional":true,"indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://onlinelibrary.wiley.com/doi/pdfdirect/10.1002/prot.22397","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5070665145","display_name":"Fumiaki Tomoike","orcid":"https://orcid.org/0000-0003-2724-2272","observed_orcids":["https://orcid.org/0000-0003-2724-2272"]},"institutions":[{"id":"https://openalex.org/I98285908","display_name":"The University of Osaka","ror":"https://ror.org/035t8zc32","country_code":"JP","type":"education","lineage":["https://openalex.org/I98285908"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Fumiaki Tomoike","raw_affiliation_strings":["Graduate School of Frontier Biological Sciences, Osaka University, Osaka 565-0871, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Graduate School of Frontier Biological Sciences, Osaka University, Osaka 565-0871, Japan","institution_ids":["https://openalex.org/I98285908"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5051688642","display_name":"Taisuke Wakamatsu","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I98285908","display_name":"The University of Osaka","ror":"https://ror.org/035t8zc32","country_code":"JP","type":"education","lineage":["https://openalex.org/I98285908"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Taisuke Wakamatsu","raw_affiliation_strings":["Graduate School of Frontier Biological Sciences, Osaka University, Osaka 565-0871, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Graduate School of Frontier Biological Sciences, Osaka University, Osaka 565-0871, Japan","institution_ids":["https://openalex.org/I98285908"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5109377309","display_name":"Noriko Nakagawa","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I4210104871","display_name":"SPring-8","ror":"https://ror.org/01d1kv753","country_code":"JP","type":"facility","lineage":["https://openalex.org/I4210104871","https://openalex.org/I4210110652","https://openalex.org/I4210111000"]},{"id":"https://openalex.org/I98285908","display_name":"The University of Osaka","ror":"https://ror.org/035t8zc32","country_code":"JP","type":"education","lineage":["https://openalex.org/I98285908"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Noriko Nakagawa","raw_affiliation_strings":["Department of Biological Sciences, Graduate School of Science, Osaka University, Osaka 560-0043, Japan","RIKEN SPring-8 Center, Hyogo 679-5148, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biological Sciences, Graduate School of Science, Osaka University, Osaka 560-0043, Japan","institution_ids":["https://openalex.org/I98285908"]},{"raw_affiliation_string":"RIKEN SPring-8 Center, Hyogo 679-5148, Japan","institution_ids":["https://openalex.org/I4210104871"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5025116997","display_name":"Seiki Kuramitsu","orcid":"https://orcid.org/0000-0003-4364-1994","observed_orcids":["https://orcid.org/0000-0003-4364-1994"]},"institutions":[{"id":"https://openalex.org/I4210104871","display_name":"SPring-8","ror":"https://ror.org/01d1kv753","country_code":"JP","type":"facility","lineage":["https://openalex.org/I4210104871","https://openalex.org/I4210110652","https://openalex.org/I4210111000"]},{"id":"https://openalex.org/I98285908","display_name":"The University of Osaka","ror":"https://ror.org/035t8zc32","country_code":"JP","type":"education","lineage":["https://openalex.org/I98285908"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Seiki Kuramitsu","raw_affiliation_strings":["Department of Biological Sciences, Graduate School of Science, Osaka University, Osaka 560-0043, Japan","Graduate School of Frontier Biological Sciences, Osaka University, Osaka 565-0871, Japan","RIKEN SPring-8 Center, Hyogo 679-5148, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biological Sciences, Graduate School of Science, Osaka University, Osaka 560-0043, Japan","institution_ids":["https://openalex.org/I98285908"]},{"raw_affiliation_string":"Graduate School of Frontier Biological Sciences, Osaka University, Osaka 565-0871, Japan","institution_ids":["https://openalex.org/I98285908"]},{"raw_affiliation_string":"RIKEN SPring-8 Center, Hyogo 679-5148, Japan","institution_ids":["https://openalex.org/I4210104871"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5072018588","display_name":"Ryoji Masui","orcid":"https://orcid.org/0000-0001-6797-5353","observed_orcids":["https://orcid.org/0000-0001-6797-5353"]},"institutions":[{"id":"https://openalex.org/I4210104871","display_name":"SPring-8","ror":"https://ror.org/01d1kv753","country_code":"JP","type":"facility","lineage":["https://openalex.org/I4210104871","https://openalex.org/I4210110652","https://openalex.org/I4210111000"]},{"id":"https://openalex.org/I98285908","display_name":"The University of Osaka","ror":"https://ror.org/035t8zc32","country_code":"JP","type":"education","lineage":["https://openalex.org/I98285908"]}],"countries":["JP"],"is_corresponding":true,"raw_author_name":"Ryoji Masui","raw_affiliation_strings":["Department of Biological Sciences, Graduate School of Science, Osaka University, Osaka 560-0043, Japan","RIKEN SPring-8 Center, Hyogo 679-5148, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biological Sciences, Graduate School of Science, Osaka University, Osaka 560-0043, Japan","institution_ids":["https://openalex.org/I98285908"]},{"raw_affiliation_string":"RIKEN SPring-8 Center, Hyogo 679-5148, Japan","institution_ids":["https://openalex.org/I4210104871"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5072018588"],"corresponding_institution_ids":["https://openalex.org/I4210104871","https://openalex.org/I98285908"],"apc_list":{"value":4550,"currency":"USD","value_usd":4550},"apc_paid":null,"fwci":0.1567,"has_fulltext":true,"cited_by_count":11,"citation_normalized_percentile":{"value":0.42617572,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":88,"max":97},"biblio":{"volume":"76","issue":"1","first_page":"244","last_page":"248"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11162","display_name":"Enzyme Structure and Function","score":0.9810000061988831,"subfield":{"id":"https://openalex.org/subfields/1315","display_name":"Structural Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T11162","display_name":"Enzyme Structure and Function","score":0.9810000061988831,"subfield":{"id":"https://openalex.org/subfields/1315","display_name":"Structural Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.007600000128149986,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10120","display_name":"Bacterial Genetics and Biotechnology","score":0.0034000000450760126,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/thermus-thermophilus-hb8","display_name":"Thermus thermophilus HB8","score":0.9750000238418579},{"id":"https://openalex.org/keywords/crystal-structure","display_name":"crystal structure","score":0.7160000205039978},{"id":"https://openalex.org/keywords/hexameric-ring","display_name":"hexameric ring","score":0.6869999766349792},{"id":"https://openalex.org/keywords/single-stranded-dna-binding","display_name":"single-stranded DNA binding","score":0.8650000095367432},{"id":"https://openalex.org/keywords/dna-repair","display_name":"DNA repair","score":0.6190000176429749},{"id":"https://openalex.org/keywords/protein-dimerization","display_name":"protein dimerization","score":0.5120000243186951},{"id":"https://openalex.org/keywords/metal-binding-proteins","display_name":"metal-binding proteins","score":0.49799999594688416},{"id":"https://openalex.org/keywords/hypothetical-protein","display_name":"hypothetical protein","score":0.3490000069141388}],"concepts":[{"id":"https://openalex.org/C2780883830","wikidata":"https://www.wikidata.org/wiki/Q139470","display_name":"Thermus thermophilus","level":4,"score":0.9787855744361877},{"id":"https://openalex.org/C203075996","wikidata":"https://www.wikidata.org/wiki/Q139677","display_name":"Operon","level":4,"score":0.5529935359954834},{"id":"https://openalex.org/C547475151","wikidata":"https://www.wikidata.org/wiki/Q25419","display_name":"Escherichia coli","level":3,"score":0.5461427569389343},{"id":"https://openalex.org/C129075420","wikidata":"https://www.wikidata.org/wiki/Q10855009","display_name":"Hypothetical protein","level":3,"score":0.5220101475715637},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.5058193206787109},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.5002567768096924},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.47605249285697937},{"id":"https://openalex.org/C199216141","wikidata":"https://www.wikidata.org/wiki/Q4995178","display_name":"Conserved sequence","level":4,"score":0.4553866386413574},{"id":"https://openalex.org/C552990157","wikidata":"https://www.wikidata.org/wiki/Q7430","display_name":"DNA","level":2,"score":0.4546116590499878},{"id":"https://openalex.org/C167625842","wikidata":"https://www.wikidata.org/wiki/Q899763","display_name":"Peptide sequence","level":3,"score":0.2169831097126007}],"mesh":[{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001426","descriptor_name":"Bacterial Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D001426","descriptor_name":"Bacterial Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D004926","descriptor_name":"Escherichia coli","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004926","descriptor_name":"Escherichia coli","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008969","descriptor_name":"Molecular Sequence Data","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016963","descriptor_name":"Thermus thermophilus","qualifier_ui":"Q000302","qualifier_name":"isolation & purification","is_major_topic":false},{"descriptor_ui":"D016963","descriptor_name":"Thermus thermophilus","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D016963","descriptor_name":"Thermus thermophilus","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D018360","descriptor_name":"Crystallography, X-Ray","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1002/prot.22397","doi":"https://doi.org/10.1002/prot.22397","is_oa":true,"landing_page_url":"https://doi.org/10.1002/prot.22397","pdf_url":"https://onlinelibrary.wiley.com/doi/pdfdirect/10.1002/prot.22397","source":{"id":"https://openalex.org/S121161810","display_name":"Proteins Structure Function and Bioinformatics","issn_l":"0887-3585","issn":["0887-3585","1097-0134"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["cwts-core","dongbi-c","doyens","jufo-1","ki-jl-1","medline","norway-1","poland-100","russia-white-list-2"],"host_organization":"https://openalex.org/P4310320595","host_organization_name":"Wiley","host_organization_lineage":["https://openalex.org/P4310320595"],"host_organization_lineage_names":["Wiley"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proteins: Structure, Function, and Bioinformatics","raw_type":"journal-article"},{"id":"pmid:19322824","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/19322824","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proteins","raw_type":"Journal Article"}],"best_oa_location":{"id":"doi:10.1002/prot.22397","doi":"https://doi.org/10.1002/prot.22397","is_oa":true,"landing_page_url":"https://doi.org/10.1002/prot.22397","pdf_url":"https://onlinelibrary.wiley.com/doi/pdfdirect/10.1002/prot.22397","source":{"id":"https://openalex.org/S121161810","display_name":"Proteins Structure Function and Bioinformatics","issn_l":"0887-3585","issn":["0887-3585","1097-0134"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["cwts-core","dongbi-c","doyens","jufo-1","ki-jl-1","medline","norway-1","poland-100","russia-white-list-2"],"host_organization":"https://openalex.org/P4310320595","host_organization_name":"Wiley","host_organization_lineage":["https://openalex.org/P4310320595"],"host_organization_lineage_names":["Wiley"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proteins: Structure, Function, and Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"study_designs":[],"awards":[],"funders":[],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2016106183.pdf","grobid_xml":"https://content.openalex.org/works/W2016106183.grobid-xml"},"referenced_works_count":19,"referenced_works":["https://openalex.org/W1510483750","https://openalex.org/W1539796472","https://openalex.org/W1568513966","https://openalex.org/W1573717502","https://openalex.org/W1583942422","https://openalex.org/W1941120413","https://openalex.org/W1983849722","https://openalex.org/W1986191025","https://openalex.org/W1990808614","https://openalex.org/W1995017064","https://openalex.org/W2001319893","https://openalex.org/W2058465275","https://openalex.org/W2069663555","https://openalex.org/W2079628454","https://openalex.org/W2097493124","https://openalex.org/W2110230147","https://openalex.org/W2123766838","https://openalex.org/W2142195509","https://openalex.org/W2148885170"],"related_works":["https://openalex.org/W2791948149","https://openalex.org/W2048891683","https://openalex.org/W1573717502","https://openalex.org/W2074858412","https://openalex.org/W2141729033","https://openalex.org/W2135319108","https://openalex.org/W2055034852","https://openalex.org/W2086155031","https://openalex.org/W2088298958"],"abstract_inverted_index":{"NIF3":[0,17,34,38,245,798,901,1203,1238,1306,1386],"family":[1,39,51,246,799,902,1204,1307,1387],"proteins":[2,40,290,440,929,1239,1292,1308,1388],"are":[3,636,643,660,1026,1069,1098,1211,1293,1409,1419,1598],"highly":[4],"conserved":[5,131,1089,1144,1182,1247,1421,1596],"from":[6,142,157,291,827,946,1008,1047],"bacteria":[7],"to":[8,217,313,349,587,604,706,811,838,880,949,1052,1101,1116,1123,1146,1160,1295,1311,1321,1334,1402,1451,1467,1485,1489,1495,1523],"human":[9,111],"[Fig.":[10,760,885,1186,1233,1263,1353,1379,1414,1422,1439],"1(A)],":[11],"but":[12,882,1487,1527],"their":[13,1102,1553],"functions":[14,287],"remain":[15],"unclear.":[16],"was":[18,81,337,406,419,509,524,560,585,594,678,692,699,712,739,754,809,913,925,1180],"originally":[19],"identified":[20],"as":[21,569,694,840,844,858,1145],"a":[22,64,86,92,116,263,292,358,491,515,824,841,859,900,1048,1397,1447,1469,1549],"NGG1-interacting":[23],"factor":[24],"in":[25,43,58,69,97,119,126,165,200,232,354,377,393,416,443,581,614,626,638,645,662,718,744,846,866,953,1037,1042,1064,1084,1213,1219,1243,1260,1350,1411,1454,1541,1552,1584],"yeast":[26],"on":[27,319,1282,1360,1566],"two-hybrid":[28],"screening.1":[29],"Several":[30,1129],"studies":[31],"of":[32,53,79,95,105,136,139,145,151,154,177,210,219,251,283,288,302,327,332,357,367,380,451,469,490,495,514,529,611,619,721,752,772,805,830,852,861,871,895,899,907,930,963,968,1000,1005,1011,1060,1080,1091,1112,1126,1138,1156,1169,1177,1193,1202,1223,1252,1275,1305,1364,1373,1376,1384,1417,1428,1436,1497,1504,1511,1544,1569,1595],"eukaryotic":[33],"homologues":[35],"suggested":[36,1576],"that":[37,76,308,782,877,927,941,1120,1174,1190,1396,1446,1461,1474,1562,1577,1592],"take":[41],"part":[42],"transcription.2,":[44],"3":[45],"The":[46,134,149,174,235,329,343,369,449,549,558,577,710,737,749,762,801,849,869,966,970,1088,1095,1108,1167,1246,1265,1381,1508],"ybgI":[47,80],"gene,":[48],"the":[49,59,77,98,137,143,146,152,166,201,204,208,211,227,233,241,244,272,284,300,311,320,324,378,404,417,452,470,479,522,538,554,570,582,589,598,606,612,615,620,627,646,655,663,667,681,703,707,742,745,806,828,853,892,896,905,921,934,942,954,958,1001,1009,1012,1034,1040,1054,1081,1085,1092,1105,1118,1124,1127,1135,1139,1151,1164,1170,1175,1178,1184,1191,1194,1199,1208,1216,1220,1224,1244,1250,1253,1257,1261,1273,1283,1302,1332,1347,1351,1361,1365,1377,1425,1429,1455,1479,1498,1502,1505,1512,1542,1545,1564,1570,1593,1599,1604],"Nif3":[50],"gene":[52,242],"Escherichia":[54],"coli,":[55],"is":[56,124,170,230,257,792,834,891,1045,1142,1196,1228,1309,1369,1394,1434,1464,1514,1518],"encoded":[57],"operon":[60],"including":[61],"endonuclease":[62],"VII,":[63],"DNA":[65,87,99,316,697,1297,1322],"repair":[66,100],"protein":[67,247,264,454,518],"involved":[68,231],"oxidative":[70],"base":[71],"damages.4":[72],"Microarray":[73],"analyses":[74],"indicated":[75,1063],"expression":[78,330],"induced":[82],"by":[83,384,391,421,701,794,815,1071,1076,1230,1371,1501],"treatment":[84],"with":[85,364,425,511,526,537,684,1030,1163,1285,1601],"damaging":[88],"agent.5":[89],"This":[90,690,790,1188,1355,1367,1491,1557],"suggests":[91,1189],"possible":[93,835,1395],"function":[94],"YbgI":[96,565],"process.":[101],"(A)":[102,965],"Sequence":[103],"alignment":[104],"TTHA1606,":[106,248],"E.":[107,178,340,563,908,931],"coli":[108,179,341,564,909,932],"YbgI,":[109],"and":[110,185,260,286,382,399,403,433,500,520,531,601,623,632,654,725,733,741,987,995,1015,1019,1033,1214,1272,1460,1534],"NIF3LI.":[112],"Human":[113],"NIF3LI":[114],"contains":[115,240,765],"PII":[117],"domain":[118,1551,1558],"its":[120],"middle":[121,1543],"region,":[122],"which":[123,169,249,1517,1547],"omitted":[125],"this":[127,296,890,1038,1043,1132,1391,1403,1412,1432,1452,1462,1475],"figure.":[128],"Asterisks":[129],"indicate":[130,1078],"residues.":[132,255],"(B)":[133,998],"structure":[135,150,301,559,751,1111,1162,1459,1503],"dimer":[138,1041,1171,1254,1378],"TTHA1606":[140,155,256,309,415,453,732,753,767,808,822,837,878,912,988,1006,1093,1113,1140,1161,1267,1483],"(viewed":[141,1007],"inside":[144,203,1010,1125,1176,1192,1509],"ring).":[147,1013],"(C)":[148,1058],"hexamer":[153,854],"viewed":[156,164,857,1046],"two":[158,195,766,773,784,862,864,1231],"sides.":[159],"[Color":[160],"figure":[161],"can":[162,855],"be":[163,812,856,939,1312,1493,1589],"online":[167],"issue,":[168],"available":[171,644,661],"at":[172,347,408,484,545,680,715,756,915,989,1249],"www.interscience.wiley.com.]":[173],"crystal":[175,473,1382,1554],"structures":[176,285,1383],"YbgI,6Staphylococcus":[180],"aureus":[181,1536],"SA1388,7Streptococcus":[182],"pneumoniae":[183],"SP1609,":[184],"Bacillus":[186],"cereus":[187,1457,1532],"YqfO8":[188],"have":[189,1240,1390],"been":[190],"determined.":[191],"In":[192,271,295,304,1206],"these":[193,1585],"structures,":[194],"metal":[196,1241,1270,1276,1299,1328],"ions":[197,1242,1277,1318,1329],"tightly":[198],"bind":[199,314,1296],"cavity":[202,1062,1359,1433,1453,1476],"hexameric":[205,842],"troid.":[206],"Although":[207,1405],"coordination":[209],"dinuclear":[212],"center":[213],"exhibits":[214],"some":[215,1578],"similarity":[216],"those":[218],"other":[220,1082],"metal-binding":[221,228,1258,1303,1348],"proteins,":[222],"it":[223,833,924],"remains":[224],"uncertain":[225],"how":[226],"site":[229,326,1259,1304,1349,1463],"function.":[234],"Thermus":[236],"thermophilus":[237,278],"HB8":[238,279],"genome":[239],"encoding":[243],"consists":[250,771],"242":[252],"amino":[253,1096,1147,1157],"acid":[254,1148,1158],"transcribed":[258],"constantly9":[259],"translated":[261],"into":[262,339,1056],"under":[265,457,650,666],"normal":[266],"growth":[267],"conditions":[268],"(unpublished":[269],"data).":[270],"\"Whole-Cell":[273],"Project,\"":[274],"we":[275,298,306,322],"selected":[276],"T.":[277],"for":[280,374,410,572,836,917,1198,1314,1521,1529],"systematic":[281],"study":[282],"all":[289,795,1385],"single":[293],"organism.10":[294],"research,":[297],"determined":[299,755,1237],"TTHA1606.":[303,328,964],"addition,":[305,1207],"found":[307,1218,1410],"has":[310,609],"ability":[312,898],"single-stranded":[315],"(ssDNA).":[317],"Based":[318],"structure,":[321],"discuss":[323],"DNA-binding":[325,897,928,1291],"plasmid":[331],"THA1606":[333],"(RIKEN":[334],"BioResource":[335],"Center)":[336],"transformed":[338],"BL21(DE3).":[342],"transformants":[344],"were":[345,371,389,441,455,535,551,747],"cultured":[346],"37\u00b0C":[348],"1":[350],"\u00d7":[351],"108":[352],"cell/mL":[353],"1.5":[355],"L":[356],"medium":[359],"containing":[360,466,506,731],"LB":[361],"broth":[362],"supplemented":[363],"50":[365,400,722],"\u03bcg/mL":[366],"ampicillin.":[368],"cells":[370,910],"then":[372,521],"incubated":[373,407],"5":[375],"h":[376],"presence":[379],"isopropyl-\u03b2-D-thiogalactopyranoside":[381],"harvested":[383],"centrifugation.":[385],"Cells":[386],"(28":[387],"g)":[388],"lysed":[390],"sonication":[392],"20":[394,444],"mM":[395,401,445,723,727],"Tris-HCl":[396,446,724],"(pH":[397,447,504],"8.0)":[398],"NaCl,":[402],"lysate":[405,906],"70\u00b0C":[409,916],"10":[411,719,918,974],"min.":[412],"After":[413],"centrifugation,":[414],"supernatant":[418],"purified":[420,807,935,1266],"successive":[422],"chromatographic":[423],"steps":[424],"Resource":[426,428],"ISO,":[427],"Q,":[429],"BioScale":[430],"CHT10-I":[431],"hydroxyapatite,":[432],"HiLoad":[434],"16/60":[435],"200":[436],"pg":[437],"columns.":[438],"Purified":[439],"stored":[442],"8.0).":[448],"crystals":[450],"obtained":[456],"condition":[458],"number":[459,669],"14":[460],"(0.1M":[461],"HEPES":[462,502,1448],"buffer,":[463],"pH":[464,729],"7.5,":[465,730],"0.2M":[467,507],"CaCl2)":[468],"Crystal":[471],"Screen":[472],"screening":[474],"kit":[475],"(Hampton":[476],"Research)":[477],"using":[478,553,562,575,597,686],"96-well":[480],"sitting-drop":[481],"vapor-diffusion":[482],"method11":[483],"20\u00b0C.":[485],"A":[486,672],"0.5":[487,512],"\u03bcL":[488,513,528,720],"aliquot":[489],"crystallization":[492],"reagent,":[493],"consisting":[494],"28%":[496],"(w/w)":[497],"PEG":[498],"400":[499],"0.1M":[501],"buffer":[503],"7.5),":[505],"CaCl2,":[508],"mixed":[510],"25":[516],"mg/mL":[517],"solution,":[519],"mixture":[523,738,972],"covered":[525],"15":[527],"silicone":[530],"paraffin":[532],"oil.":[533],"Data":[534,648],"collected":[536],"RIKEN":[539],"Structural":[540],"Genomics":[541],"Beamline":[542],"II":[543],"(BL26B2)12":[544],"SPring-8":[546],"(Hyogo,":[547],"Japan).":[548],"data":[550,634,658],"processed":[552,633],"HKL-2000":[555],"program":[556,583],"suite.13":[557],"solved":[561],"(PDB":[566],"code":[567,652],"1NMP)":[568],"model":[571,608],"molecular":[573,803],"replacement":[574],"Molrep.14":[576],"automatic":[578],"tracing":[579],"procedure":[580],"ARP/wARP15":[584],"utilized":[586],"build":[588],"initial":[590],"model.":[591],"Model":[592],"refinement":[593],"carried":[595,713],"out":[596,714],"programs":[599],"Xtalview16":[600],"CNS.17":[602],"According":[603],"PROCHECK,18":[605],"final":[607],"85.2%":[610],"residues":[613,625,1079,1210,1372,1408,1438,1597],"most":[616,1416],"favored":[617],"region":[618,1090,1248,1344,1356,1368,1413],"Ramachandran":[621],"plot":[622],"no":[624,1269,1279],"disallowed":[628],"regions.":[629],"Data-collection":[630],"statistics":[631,635],"presented":[637],"Table":[639],"I.":[640],"(The":[641],"coordinates":[642],"Protein":[647],"Bank":[649],"accession":[651,668],"2YYB":[653],"nucleotide":[656],"sequence":[657,1149],"reported":[659,1445],"DDBJ/EMBL/GenBank":[664,670],"databases":[665],"AP008226.)":[671],"synthesized":[673],"37-mer":[674],"oligonucleotide":[675,691,705],"(5\u2032-ATGTGAATC":[676],"AGTATGGTTACTATCTGCTGAAGGAAAT-3\u2032)":[677],"labeled":[679,704],"5\u2032":[682],"end":[683],"[\u03b3-32P]ATP":[685],"T4":[687],"polynucleotide":[688],"kinase.":[689],"used":[693],"ssDNA.":[695],"Double-stranded":[696],"(dsDNA)":[698],"made":[700],"annealing":[702],"complementary":[708],"oligonucleotide.":[709],"reaction":[711,971],"room":[716],"temperature":[717],"100":[726],"KCl,":[728],"ssDNA":[734,881,976,1121,1286,1522],"or":[735,961,981,1324,1339,1602],"dsDNA.":[736,1490,1530],"electrophoresed":[740],"bands":[743],"gel":[746,816],"analyzed.":[748],"overall":[750,850],"2.6":[757],"\u00c5":[758],"resolution":[759],"1(B)].":[761],"asymmetric":[763],"unit":[764,1172],"molecules.":[768],"Each":[769],"subunit":[770,1083],"interlinked":[774],"\u03b1/\u03b2":[775],"domains.":[776],"Both":[777],"domains":[778],"comprise":[779],"three":[780],"layers,":[781],"is,":[783],"\u03b1-helix":[785],"layers":[786],"sandwiching":[787],"one":[788,947],"\u03b2-sheet.":[789],"fold":[791],"shared":[793],"structurally":[796,1236],"characterized":[797],"proteins.6-8":[800],"apparent":[802,1280],"mass":[804],"estimated":[810],"\u223c180":[813],"kDa":[814],"filtration":[817],"(data":[818,1287],"not":[819,883,1288,1488,1528],"shown),":[820],"suggesting":[821],"forms":[823,1548,1559],"hexamer.":[825],"Judging":[826],"result":[829],"crystallographic":[831],"analysis,":[832],"exist":[839],"form,":[843],"shown":[845],"Figure":[847,1031],"1(C).":[848],"shape":[851],"double-ring":[860],"trimers:":[863],"trimers":[865],"face-to-face":[867],"contact.":[868],"results":[870,967],"electrophoretic":[872],"mobility-shift":[873],"assay":[874],"(EMSA)":[875],"showed":[876],"bound":[879,1450,1484],"dsDNA":[884,982],"2(A)].":[886],"To":[887],"our":[888],"knowledge,":[889],"first":[893],"report":[894],"protein.":[903],"Since":[904],"overexpressing":[911],"heated":[914],"min":[919],"during":[920],"purification":[922],"process,":[923],"unlikely":[926],"contaminated":[933],"preparations.":[936],"It":[937,1393,1587],"should":[938,1588],"noted":[940,1591],"binding":[943,1333,1506],"affinity":[944],"varied":[945],"preparation":[948],"another.":[950],"Some":[951],"factors":[952],"preparations":[955],"might":[956,1492,1580],"affect":[957,1331],"structural":[959],"stability":[960],"activity":[962],"EMSA.":[969],"contained":[973,1268],"nM":[975],"(the":[977,983],"left":[978],"six":[979,985],"lanes)":[980,986],"right":[984],"0,":[990],"4.5,":[991],"9,":[992],"18,":[993],"36,":[994],"40":[996],"\u03bcM.":[997],"Stereoview":[999,1059],"electrostatic":[1002],"potential":[1003],"map":[1004],"Red":[1014],"blue":[1016],"represent":[1017],"negatively":[1018,1398],"positively":[1020,1342],"charged":[1021,1343,1399],"regions,":[1022],"respectively.":[1023],"Two":[1024],"cavities":[1025],"also":[1027,1389,1477,1590],"indicated.":[1028],"Compared":[1029],"1(B)":[1032],"panel":[1035,1044,1065],"D":[1036],"figure,":[1039],"slightly":[1049],"different":[1050],"angle":[1051],"bring":[1053],"cleft":[1055,1227,1262,1352,1430],"view.":[1057],"another":[1061,1358],"B.":[1066,1456,1531],"Side":[1067],"chains":[1068],"represented":[1070],"sticks.":[1072],"Residue":[1073],"numbers":[1074],"followed":[1075],"asterisks":[1077],"dimer.":[1086,1094],"(D)":[1087],"acids":[1097],"colored":[1099],"according":[1100],"conservation;":[1103],"see":[1104],"color-coding":[1106],"bar.":[1107],"troidal":[1109,1571],"ring":[1110,1141,1179,1195,1513],"prompted":[1114],"us":[1115],"examine":[1117],"possibility":[1119],"binds":[1122,1401],"ring.":[1128],"observations":[1130,1472],"support":[1131],"hypothesis.":[1133],"First,":[1134],"inner":[1136,1221],"surface":[1137,1222],"more":[1143,1181],"than":[1150,1183],"outside.":[1152],"We":[1153],"mapped":[1154],"levels":[1155],"conservation":[1159],"ConSurf":[1165],"server.19":[1166],"mapping":[1168],"revealed":[1173],"outside":[1185],"2(D)].":[1187,1264,1423,1440],"important":[1197,1313],"functional":[1200],"roles":[1201],"proteins.":[1205],"well-conserved":[1209,1437],"concentrated":[1212],"near":[1215,1346,1431],"clefts":[1217],"ring:":[1225],"each":[1226],"formed":[1229,1370],"subunits":[1232,1375],"2(B)].":[1234,1354],"Other":[1235],"cleft.6-8":[1245],"interface":[1251],"partially":[1255],"overlaps":[1256],"ion,":[1271],"addition":[1274],"had":[1278],"effect":[1281],"interaction":[1284],"shown).":[1289],"Many":[1290],"known":[1294],"without":[1298,1603],"ion.":[1300],"However,":[1301,1424],"presumed":[1310],"unassigned":[1315],"functions.":[1316],"Metal":[1317],"may":[1319,1330],"contribute":[1320],"sequence-":[1323],"length-specific":[1325],"binding.":[1326],"Alternatively,":[1327],"mRNA,":[1335],"modified":[1336],"nucleic":[1337],"acids,":[1338],"polyphosphates.":[1340],"Second,":[1341],"exists":[1345],"comprises":[1357,1478],"opposite":[1362],"side":[1363,1426,1568],"cleft.":[1366],"both":[1374],"2(C)].":[1380],"cavity.":[1392,1404],"ligand":[1400,1499,1579],"many":[1406],"basic":[1407],"2(C)],":[1415],"them":[1418],"less":[1420],"wall":[1427],"composed":[1435],"Interestingly,":[1441],"Godsey":[1442,1573],"et":[1443,1574],"al.":[1444,1575],"molecule":[1449],"YqfO":[1458,1533],"large":[1465,1519],"enough":[1466,1520],"accommodate":[1468],"nucleotide.8":[1470],"These":[1471],"imply":[1473],"ligand-binding":[1480],"site.":[1481,1507],"Finally,":[1482],"ssDNA,":[1486],"due":[1494],"restriction":[1496],"size":[1500],"diameter":[1510],"\u223c24":[1515],"\u00c5,":[1516],"pass":[1524],"through":[1525],"it,":[1526],"S.":[1535],"SA1388":[1537],"contain":[1538],"an":[1539],"insert":[1540],"protein,":[1546],"PII-like":[1550],"structures.7,":[1555],"8":[1556],"trimeric":[1560],"lids":[1561],"cover":[1563],"openings":[1565],"either":[1567],"rings.":[1572],"cause":[1581],"conformational":[1582],"change":[1583],"lids.8":[1586],"pattern":[1594],"same":[1600],"lids.":[1605]},"counts_by_year":[{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":4},{"year":2018,"cited_by_count":1},{"year":2014,"cited_by_count":4},{"year":2012,"cited_by_count":1}],"updated_date":"2026-11-14T11:04:58.165337","created_date":"2016-06-24T00:00:00"}
