2DEM
| Crystal structure of Uracil-DNA glycosylase in complex with AP:A containing DNA | Descriptor: | 5'-D(*AP*TP*GP*TP*TP*GP*CP*(D1P)P*TP*TP*AP*GP*TP*CP*C)-3', 5'-D(*GP*GP*AP*CP*TP*AP*AP*AP*GP*CP*AP*AP*CP*A)-3', DIHYDROGENPHOSPHATE ION, ... | Authors: | Kosaka, H, Nakagawa, N, Masui, R, Hoseki, J, Kuramitsu, S, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | Deposit date: | 2006-02-13 | Release date: | 2007-04-24 | Last modified: | 2023-10-25 | Method: | X-RAY DIFFRACTION (1.95 Å) | Cite: | Crystal structure of family 5 uracil-DNA glycosylase bound to DNA. J.Mol.Biol., 373, 2007
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2E6X
| X-ray structure of TT1592 from Thermus thermophilus HB8 | Descriptor: | Hypothetical protein TTHA1281 | Authors: | Yamada, M, Nakagawa, N, Kanagawa, M, Kuramitsu, S, Kamitori, S, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | Deposit date: | 2007-01-05 | Release date: | 2007-12-18 | Last modified: | 2011-07-13 | Method: | X-RAY DIFFRACTION (2 Å) | Cite: | X-ray structure of TT1592 from Thermus thermophilus HB8 To be Published
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2E6K
| X-ray structure of Thermus thermopilus HB8 TT0505 | Descriptor: | Transketolase | Authors: | Yoshida, H, Kamitori, S, Agari, Y, Iino, H, Kanagawa, M, Nakagawa, N, Ebihara, A, Kuramitsu, S, Yokoyama, S, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | Deposit date: | 2006-12-27 | Release date: | 2007-11-13 | Last modified: | 2023-11-15 | Method: | X-RAY DIFFRACTION (2.09 Å) | Cite: | X-ray structure of Thermus thermophilus HB8 TT0505 To be Published
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3AUO
| DNA polymerase X from Thermus thermophilus HB8 ternary complex with 1-nt gapped DNA and ddGTP | Descriptor: | 1-nt gapped DNA, 2'-3'-DIDEOXYGUANOSINE-5'-TRIPHOSPHATE, DNA polymerase beta family (X family), ... | Authors: | Nakane, S, Nakagawa, N, Masui, R, Kuramitsu, S, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | Deposit date: | 2011-02-11 | Release date: | 2012-01-25 | Last modified: | 2023-11-01 | Method: | X-RAY DIFFRACTION (2.7 Å) | Cite: | The structural basis of the kinetic mechanism of a gap-filling X-family DNA polymerase that binds Mg(2+)-dNTP before binding to DNA. J.Mol.Biol., 417, 2012
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3B0Y
| K263D mutant of PolX from Thermus thermophilus HB8 complexed with Ca-dGTP | Descriptor: | 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE, CALCIUM ION, CHLORIDE ION, ... | Authors: | Nakane, S, Nakagawa, N, Masui, R, Kuramitsu, S, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | Deposit date: | 2011-06-17 | Release date: | 2012-05-02 | Last modified: | 2023-11-01 | Method: | X-RAY DIFFRACTION (1.45 Å) | Cite: | The structural basis of the kinetic mechanism of a gap-filling X-family DNA polymerase that binds Mg(2+)-dNTP before binding to DNA. J.Mol.Biol., 417, 2012
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3B0X
| K263A mutant of PolX from Thermus thermophilus HB8 complexed with Ca-dGTP | Descriptor: | 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE, CALCIUM ION, CHLORIDE ION, ... | Authors: | Nakane, S, Nakagawa, N, Masui, R, Kuramitsu, S, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | Deposit date: | 2011-06-17 | Release date: | 2012-05-02 | Last modified: | 2023-11-01 | Method: | X-RAY DIFFRACTION (1.36 Å) | Cite: | The structural basis of the kinetic mechanism of a gap-filling X-family DNA polymerase that binds Mg(2+)-dNTP before binding to DNA. J.Mol.Biol., 417, 2012
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2ZXP
| Crystal structure of RecJ in complex with Mn2+ from Thermus thermophilus HB8 | Descriptor: | MANGANESE (II) ION, Single-stranded DNA specific exonuclease RecJ | Authors: | Wakamatsu, T, Kitamura, Y, Nakagawa, N, Masui, R, Kuramitsu, S. | Deposit date: | 2009-01-05 | Release date: | 2010-01-05 | Last modified: | 2023-11-01 | Method: | X-RAY DIFFRACTION (2.3 Å) | Cite: | Structure of RecJ exonuclease defines its specificity for single-stranded DNA J.Biol.Chem., 285, 2010
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3A0J
| Crystal structure of cold shock protein 1 from Thermus thermophilus HB8 | Descriptor: | Cold shock protein | Authors: | Miyazaki, T, Nakagawa, N, Kuramitsu, S, Masui, R, Yokoyama, S, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | Deposit date: | 2009-03-19 | Release date: | 2010-03-23 | Last modified: | 2023-11-01 | Method: | X-RAY DIFFRACTION (1.65 Å) | Cite: | The Biological Action of Cold Shock Protein 1 from Thermus thermophilus HB8 To be Published
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3AAM
| Crystal structure of endonuclease IV from Thermus thermophilus HB8 | Descriptor: | Endonuclease IV, MANGANESE (II) ION, PHOSPHATE ION | Authors: | Asano, R, Ishikawa, H, Nakane, S, Baba, S, Nakagawa, N, Kuramitsu, S, Masui, R, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | Deposit date: | 2009-11-20 | Release date: | 2010-12-01 | Last modified: | 2023-11-01 | Method: | X-RAY DIFFRACTION (1.58 Å) | Cite: | An additional C-terminal loop in endonuclease IV, an apurinic/apyrimidinic endonuclease, controls binding affinity to DNA Acta Crystallogr.,Sect.D, 67, 2011
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3A4Y
| Crystal Structure of H61A mutant TTHA0252 from Thermus thermophilus HB8 | Descriptor: | CITRATE ANION, Ribonuclease TTHA0252, SULFATE ION, ... | Authors: | Ishikawa, H, Nakagawa, N, Kuramitsu, S, Yokoyama, S, Masui, R, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | Deposit date: | 2009-07-22 | Release date: | 2009-08-04 | Last modified: | 2023-11-01 | Method: | X-RAY DIFFRACTION (2.5 Å) | Cite: | Crystal Structure of H61A mutant TTHA0252 from Thermus thermophilus HB8 to be published
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2ZXR
| Crystal structure of RecJ in complex with Mg2+ from Thermus thermophilus HB8 | Descriptor: | MAGNESIUM ION, Single-stranded DNA specific exonuclease RecJ | Authors: | Wakamatsu, T, Kitamura, Y, Nakagawa, N, Masui, R, Kuramitsu, S. | Deposit date: | 2009-01-05 | Release date: | 2010-01-05 | Last modified: | 2023-11-01 | Method: | X-RAY DIFFRACTION (2.15 Å) | Cite: | Structure of RecJ exonuclease defines its specificity for single-stranded DNA J.Biol.Chem., 285, 2010
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3AAL
| Crystal Structure of endonuclease IV from Geobacillus kaustophilus | Descriptor: | CACODYLATE ION, FE (III) ION, Probable endonuclease 4, ... | Authors: | Asano, R, Ishikawa, H, Nakane, S, Nakagawa, N, Kuramitsu, S, Masui, R, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | Deposit date: | 2009-11-20 | Release date: | 2010-12-01 | Last modified: | 2023-11-01 | Method: | X-RAY DIFFRACTION (1.6 Å) | Cite: | An additional C-terminal loop in endonuclease IV, an apurinic/apyrimidinic endonuclease, controls binding affinity to DNA Acta Crystallogr.,Sect.D, 67, 2011
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3AF6
| The crystal structure of an archaeal CPSF subunit, PH1404 from Pyrococcus horikoshii complexed with RNA-analog | Descriptor: | 5'-R(*(SSU)P*(SSU)P*(SSU)P*(SSU)P*(SSU)P*(SSU))-3', Putative uncharacterized protein PH1404, SULFATE ION, ... | Authors: | Nishida, Y, Ishikawa, H, Nakagawa, N, Masui, R, Kuramitsu, S. | Deposit date: | 2010-02-24 | Release date: | 2010-04-21 | Last modified: | 2023-11-01 | Method: | X-RAY DIFFRACTION (2.6 Å) | Cite: | Crystal structure of an archaeal cleavage and polyadenylation specificity factor subunit from Pyrococcus horikoshii Proteins, 78, 2010
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3AKD
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3ADR
| The first crystal structure of an archaeal metallo-beta-lactamase superfamily protein; ST1585 from Sulfolobus tokodaii | Descriptor: | 1,2-ETHANEDIOL, 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID, Putative uncharacterized protein ST1585, ... | Authors: | Shimada, A, Ishikawa, H, Nakagawa, N, Kuramitsu, S, Masui, R. | Deposit date: | 2010-01-28 | Release date: | 2010-04-21 | Last modified: | 2017-10-11 | Method: | X-RAY DIFFRACTION (1.8 Å) | Cite: | The first crystal structure of an archaeal metallo-beta-lactamase superfamily protein; ST1585 from Sulfolobus tokodaii Proteins, 78, 2010
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3AF5
| The crystal structure of an archaeal CPSF subunit, PH1404 from Pyrococcus horikoshii | Descriptor: | ACETIC ACID, Putative uncharacterized protein PH1404, SULFATE ION, ... | Authors: | Nishida, Y, Ishikawa, H, Nakagawa, N, Masui, R, Kuramitsu, S. | Deposit date: | 2010-02-23 | Release date: | 2010-04-21 | Last modified: | 2024-03-13 | Method: | X-RAY DIFFRACTION (2.6 Å) | Cite: | Crystal structure of an archaeal cleavage and polyadenylation specificity factor subunit from Pyrococcus horikoshii Proteins, 78, 2010
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3AKC
| Crystal structure of CMP kinase in complex with CDP and ADP from Thermus thermophilus HB8 | Descriptor: | ADENOSINE-5'-DIPHOSPHATE, CYTIDINE-5'-DIPHOSPHATE, Cytidylate kinase, ... | Authors: | Mega, R, Nakagawa, N, Kuramitsu, S, Masui, R. | Deposit date: | 2010-07-12 | Release date: | 2011-07-06 | Last modified: | 2023-11-01 | Method: | X-RAY DIFFRACTION (1.65 Å) | Cite: | The crystal structure of the tertiary complex of CMP kinase with a phosphoryl group acceptor and a donor from Thermus thermophilus HB8 To be Published
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3AV3
| Crystal structure of glycinamide ribonucleotide transformylase 1 from Geobacillus kaustophilus | Descriptor: | MAGNESIUM ION, Phosphoribosylglycinamide formyltransferase | Authors: | Kanagawa, M, Baba, S, Nakagawa, N, Ebihara, A, Kuramitsu, S, Yokoyama, S, Sampei, G, Kawai, G, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | Deposit date: | 2011-02-18 | Release date: | 2012-03-07 | Last modified: | 2014-01-15 | Method: | X-RAY DIFFRACTION (1.7 Å) | Cite: | Structures and reaction mechanisms of the two related enzymes, PurN and PurU. J.Biochem., 154, 2013
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3ASZ
| CMP-complex structure of uridine kinase from Thermus thermophilus HB8 | Descriptor: | CYTIDINE-5'-MONOPHOSPHATE, Uridine kinase | Authors: | Tomoike, F, Nakagawa, N, Kuramitsu, S, Masui, R. | Deposit date: | 2010-12-22 | Release date: | 2011-06-01 | Last modified: | 2024-04-03 | Method: | X-RAY DIFFRACTION (2.25 Å) | Cite: | A Single Amino Acid Limits the Substrate Specificity of Thermus thermophilus Uridine-Cytidine Kinase to Cytidine Biochemistry, 50, 2011
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3AU2
| DNA polymerase X from Thermus thermophilus HB8 complexed with Ca-dGTP | Descriptor: | 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE, CALCIUM ION, CHLORIDE ION, ... | Authors: | Nakane, S, Ishikawa, H, Wakamatsu, T, Nakagawa, N, Masui, R, Kuramitsu, S, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | Deposit date: | 2011-01-28 | Release date: | 2012-01-25 | Last modified: | 2024-03-13 | Method: | X-RAY DIFFRACTION (1.4 Å) | Cite: | The structural basis of the kinetic mechanism of a gap-filling X-family DNA polymerase that binds Mg(2+)-dNTP before binding to DNA. J.Mol.Biol., 417, 2012
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3ASY
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3AW8
| Crystal structure of N5-carboxyaminoimidazole ribonucleotide synthetase from Thermus thermophilus HB8 | Descriptor: | ADENOSINE MONOPHOSPHATE, CHLORIDE ION, Phosphoribosylaminoimidazole carboxylase, ... | Authors: | Okada, K, Tsunoda, S, Taka, H, Baba, S, Kanagawa, M, Nakagawa, N, Ebihara, A, Kuramitsu, S, Yokoyama, S, Kawai, G, Sampei, G, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | Deposit date: | 2011-03-15 | Release date: | 2012-04-11 | Last modified: | 2024-03-13 | Method: | X-RAY DIFFRACTION (2.6 Å) | Cite: | Crystal structures of N5-carboxyaminoimidazole ribonucleotide synthetase, PurK, from thermophilic bacteria To be Published
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3AX6
| Crystal structure of N5-carboxyaminoimidazole ribonucleotide synthetase from Thermotoga maritima | Descriptor: | ADENOSINE-5'-DIPHOSPHATE, Phosphoribosylaminoimidazole carboxylase, ATPase subunit | Authors: | Miyazawa, R, Kanagawa, M, Baba, S, Nakagawa, N, Ebihara, A, Kuramitsu, S, Yokoyama, S, Kawai, G, Sampei, G, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | Deposit date: | 2011-03-30 | Release date: | 2012-04-25 | Method: | X-RAY DIFFRACTION (2.2 Å) | Cite: | Crystal structures of N5-carboxyaminoimidazole ribonucleotide synthetase, PurK, from thermophilic bacteria To be Published
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3W34
| Ternary complex of Thermus thermophilus HB8 uridine-cytidine kinase with substrates | Descriptor: | 4-AMINO-1-BETA-D-RIBOFURANOSYL-2(1H)-PYRIMIDINONE, PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER, Uridine kinase | Authors: | Tomoike, F, Nakagawa, N, Masui, R, Kuramitsu, S. | Deposit date: | 2012-12-10 | Release date: | 2013-12-11 | Last modified: | 2024-03-20 | Method: | X-RAY DIFFRACTION (1.91 Å) | Cite: | Structural and Biochemical Studies on the Reaction Mechanism of Uridine-Cytidine Kinase Protein J., 34, 2015
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3W5W
| Mn2+-GMP complex of nanoRNase (Nrn) from Bacteroides fragilis | Descriptor: | GUANOSINE-5'-MONOPHOSPHATE, MANGANESE (II) ION, Putative exopolyphosphatase-related protein | Authors: | Uemura, Y, Nakagawa, N, Wakamatsu, T, Montelione, G.T, Hunt, J.F, Masui, R, Kuramitsu, S. | Deposit date: | 2013-02-07 | Release date: | 2013-07-10 | Last modified: | 2023-11-08 | Method: | X-RAY DIFFRACTION (2.95 Å) | Cite: | Crystal structure of the ligand-binding form of nanoRNase from Bacteroides fragilis, a member of the DHH/DHHA1 phosphoesterase family of proteins. Febs Lett., 587, 2013
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