6JY0
| CryoEM structure of S.typhimurium R-type straight flagellar filament made of FljB (A461V) | Descriptor: | Flagellin | Authors: | Yamaguchi, T, Toma, S, Terahara, N, Miyata, T, Minamino, T, Ashikara, M, Namba, K, Kato, T. | Deposit date: | 2019-04-25 | Release date: | 2020-02-19 | Last modified: | 2024-03-27 | Method: | ELECTRON MICROSCOPY (3.56 Å) | Cite: | Structural and Functional Comparison ofSalmonellaFlagellar Filaments Composed of FljB and FliC. Biomolecules, 10, 2020
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4YL4
| 1.1 Angstrom resolution X-ray Crystallographic Structure of Psudoazurin | Descriptor: | COPPER (II) ION, GLYCEROL, Pseudoazurin | Authors: | Yamaguchi, T, Asamura, S, Takashina, A, Unno, M, Kohzuma, T. | Deposit date: | 2015-03-05 | Release date: | 2016-03-09 | Last modified: | 2023-11-08 | Method: | X-RAY DIFFRACTION (1.1 Å) | Cite: | X-ray crystallographic evidence for the simultaneous presence of axial and rhombic sites in cupredoxins: atomic resolution X-ray crystal structure analysis of pseudoazurin and DFT modelling Rsc Adv, 6, 2016
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7CLR
| CryoEM structure of S.typhimurium flagellar LP ring | Descriptor: | Flagellar L-ring protein, Flagellar P-ring protein | Authors: | Yamaguchi, T, Makino, F, Miyata, T, Minamino, T, Kato, T, Namba, K. | Deposit date: | 2020-07-21 | Release date: | 2021-06-02 | Last modified: | 2021-12-22 | Method: | ELECTRON MICROSCOPY (3.5 Å) | Cite: | Structure of the molecular bushing of the bacterial flagellar motor. Nat Commun, 12, 2021
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5XMO
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5Y23
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5WV4
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4WDT
| 17beta-HSD5 in complex with 2-nitro-5-(phenylsulfonyl)phenol | Descriptor: | 2-nitro-5-(phenylsulfonyl)phenol, Aldo-keto reductase family 1 member C3, NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE | Authors: | Amano, Y, Yamaguchi, T. | Deposit date: | 2014-09-09 | Release date: | 2015-04-15 | Last modified: | 2024-06-26 | Method: | X-RAY DIFFRACTION (1.5 Å) | Cite: | Structures of complexes of type 5 17 beta-hydroxysteroid dehydrogenase with structurally diverse inhibitors: insights into the conformational changes upon inhibitor binding. Acta Crystallogr.,Sect.D, 71, 2015
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4WDU
| 17beta-HSD5 in complex with 4-chloro-N-(4-chlorobenzyl)-5-nitro-1H-pyrazole-3-carboxamide | Descriptor: | 4-chloro-N-(4-chlorobenzyl)-5-nitro-1H-pyrazole-3-carboxamide, Aldo-keto reductase family 1 member C3, NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE | Authors: | Amano, Y, Yamaguchi, T. | Deposit date: | 2014-09-09 | Release date: | 2015-04-15 | Last modified: | 2024-05-29 | Method: | X-RAY DIFFRACTION (1.7 Å) | Cite: | Structures of complexes of type 5 17 beta-hydroxysteroid dehydrogenase with structurally diverse inhibitors: insights into the conformational changes upon inhibitor binding. Acta Crystallogr.,Sect.D, 71, 2015
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4WDX
| 17beta-HSD5 in complex with [4-(2-hydroxyethyl)piperidin-1-yl](5-methyl-1H-indol-2-yl)methanone | Descriptor: | Aldo-keto reductase family 1 member C3, NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE, [4-(2-hydroxyethyl)piperidin-1-yl](5-methyl-1H-indol-2-yl)methanone | Authors: | Amano, Y, Yamaguchi, T. | Deposit date: | 2014-09-09 | Release date: | 2015-04-15 | Last modified: | 2024-05-29 | Method: | X-RAY DIFFRACTION (1.64 Å) | Cite: | Structures of complexes of type 5 17 beta-hydroxysteroid dehydrogenase with structurally diverse inhibitors: insights into the conformational changes upon inhibitor binding. Acta Crystallogr.,Sect.D, 71, 2015
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4WDW
| 17beta-HSD5 in complex with 3,6-dihydropyridin-1(2H)-yl(5-methyl-1H-indol-2-yl)methanone | Descriptor: | 3,6-dihydropyridin-1(2H)-yl(5-methyl-1H-indol-2-yl)methanone, Aldo-keto reductase family 1 member C3, NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE | Authors: | Amano, Y, Yamaguchi, T. | Deposit date: | 2014-09-09 | Release date: | 2015-04-15 | Last modified: | 2024-05-29 | Method: | X-RAY DIFFRACTION (1.94 Å) | Cite: | Structures of complexes of type 5 17 beta-hydroxysteroid dehydrogenase with structurally diverse inhibitors: insights into the conformational changes upon inhibitor binding. Acta Crystallogr.,Sect.D, 71, 2015
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2NVL
| Crystal structure of archaeal peroxiredoxin, thioredoxin peroxidase from Aeropyrum pernix K1 (sulfonic acid form) | Descriptor: | Probable peroxiredoxin | Authors: | Nakamura, T, Yamamoto, T, Abe, M, Matsumura, H, Hagihara, Y, Goto, T, Yamaguchi, T, Inoue, T. | Deposit date: | 2006-11-13 | Release date: | 2007-11-20 | Last modified: | 2023-11-15 | Method: | X-RAY DIFFRACTION (2.36 Å) | Cite: | Oxidation of archaeal peroxiredoxin involves a hypervalent sulfur intermediate Proc.Natl.Acad.Sci.Usa, 105, 2008
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7BOW
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7BPO
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7BR1
| Hydroxynitrile lyase from Parafontaria laminate complexed with benzaldehyde prepared by cocrystallization | Descriptor: | 1,2-ETHANEDIOL, Hydroxynitrile lyase, THIOCYANATE ION, ... | Authors: | Nuylert, A, Nakabayashi, M, Yamaguchi, T, Asano, Y. | Deposit date: | 2020-03-26 | Release date: | 2021-04-07 | Last modified: | 2023-11-29 | Method: | X-RAY DIFFRACTION (1.25 Å) | Cite: | Hydroxynitrile lyase from Parafonteria laminate complexed with benzaldehyde prepared by cocrystallization To Be Published
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8HIS
| Crystal structure of DNA decamer containing GuNA[Me,tBu] | Descriptor: | CACODYLIC ACID, DNA (5'-D(*GP*CP*GP*TP*AP*(LR6)P*AP*CP*GP*C)-3') | Authors: | Aoyama, H, Obika, S, Yamaguchi, T. | Deposit date: | 2022-11-21 | Release date: | 2023-08-09 | Last modified: | 2023-09-06 | Method: | X-RAY DIFFRACTION (2.01 Å) | Cite: | Mechanism of the extremely high duplex-forming ability of oligonucleotides modified with N-tert-butylguanidine- or N-tert-butyl-N'- methylguanidine-bridged nucleic acids. Nucleic Acids Res., 51, 2023
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8HM9
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8I50
| Crystal structure of DNA octamer containing GuNA[Me,Me] | Descriptor: | DNA (5'-D(*GP*(OIQ)P*GP*(BRU)P*AP*CP*AP*C)-3') | Authors: | Aoyama, H, Obika, S, Yamaguchi, T. | Deposit date: | 2023-01-21 | Release date: | 2023-08-09 | Last modified: | 2023-09-06 | Method: | X-RAY DIFFRACTION (0.95 Å) | Cite: | Mechanism of the extremely high duplex-forming ability of oligonucleotides modified with N-tert-butylguanidine- or N-tert-butyl-N'- methylguanidine-bridged nucleic acids. Nucleic Acids Res., 51, 2023
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8HU5
| Crystal structure of DNA octamer containing GuNA[Me,tBu] | Descriptor: | DNA (5'-D(*GP*(LR6)P*GP*(BRU)P*AP*CP*AP*C)-3') | Authors: | Aoyama, H, Obika, H, Yamaguchi, T. | Deposit date: | 2022-12-22 | Release date: | 2023-08-09 | Last modified: | 2023-09-06 | Method: | X-RAY DIFFRACTION (0.93 Å) | Cite: | Mechanism of the extremely high duplex-forming ability of oligonucleotides modified with N-tert-butylguanidine- or N-tert-butyl-N'- methylguanidine-bridged nucleic acids. Nucleic Acids Res., 51, 2023
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6AKN
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6KNF
| CryoEM map and model of Nitrite Reductase at pH 6.2 | Descriptor: | COPPER (II) ION, Copper-containing nitrite reductase | Authors: | Adachi, N, Yamaguchi, T, Moriya, T, Kawasaki, M, Koiwai, K, Shinoda, A, Yamada, Y, Yumoto, F, Kohzuma, T, Senda, T. | Deposit date: | 2019-08-05 | Release date: | 2020-08-12 | Last modified: | 2024-05-29 | Method: | ELECTRON MICROSCOPY (2.99 Å) | Cite: | 2.85 and 2.99 angstrom resolution structures of 110 kDa nitrite reductase determined by 200 kV cryogenic electron microscopy. J.Struct.Biol., 213, 2021
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6KNG
| CryoEM map and model of Nitrite Reductase at pH 8.1 | Descriptor: | COPPER (II) ION, Copper-containing nitrite reductase | Authors: | Adachi, N, Yamaguchi, T, Moriya, T, Kawasaki, M, Koiwai, K, Shinoda, A, Yamada, Y, Yumoto, F, Kohzuma, T, Senda, T. | Deposit date: | 2019-08-05 | Release date: | 2020-08-12 | Last modified: | 2024-05-29 | Method: | ELECTRON MICROSCOPY (2.85 Å) | Cite: | 2.85 and 2.99 angstrom resolution structures of 110 kDa nitrite reductase determined by 200 kV cryogenic electron microscopy. J.Struct.Biol., 213, 2021
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4XVD
| 17beta-HSD5 in complex with 4-nitro-2-({4-[3-(trifluoromethyl)phenyl]piperazin-1-yl}methyl)phenol | Descriptor: | 4-nitro-2-({4-[3-(trifluoromethyl)phenyl]piperazin-1-yl}methyl)phenol, Aldo-keto reductase family 1 member C3, NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE | Authors: | Amano, Y, Yamaguchi, T, Niimi, T, Sakashita, H. | Deposit date: | 2015-01-27 | Release date: | 2015-04-15 | Last modified: | 2023-11-08 | Method: | X-RAY DIFFRACTION (2.81 Å) | Cite: | Structures of complexes of type 5 17 beta-hydroxysteroid dehydrogenase with structurally diverse inhibitors: insights into the conformational changes upon inhibitor binding. Acta Crystallogr.,Sect.D, 71, 2015
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5D9D
| Luciferin-regenerating enzyme solved by SAD using synchrotron radiation at room temperature | Descriptor: | (4S)-2-METHYL-2,4-PENTANEDIOL, Luciferin regenerating enzyme, MAGNESIUM ION, ... | Authors: | Yamashita, K, Pan, D, Okuda, T, Murai, T, Kodan, A, Yamaguchi, T, Gomi, K, Kajiyama, N, Kato, H, Ago, H, Yamamoto, M, Nakatsu, T. | Deposit date: | 2015-08-18 | Release date: | 2015-09-23 | Last modified: | 2024-03-20 | Method: | X-RAY DIFFRACTION (1.701 Å) | Cite: | An isomorphous replacement method for efficient de novo phasing for serial femtosecond crystallography. Sci Rep, 5, 2015
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5D9B
| Luciferin-regenerating enzyme solved by SIRAS using XFEL (refined against native data) | Descriptor: | (4S)-2-METHYL-2,4-PENTANEDIOL, Luciferin regenerating enzyme, MAGNESIUM ION | Authors: | Yamashita, K, Pan, D, Okuda, T, Murai, T, Kodan, A, Yamaguchi, T, Gomi, K, Kajiyama, N, Kato, H, Ago, H, Yamamoto, M, Nakatsu, T. | Deposit date: | 2015-08-18 | Release date: | 2015-09-23 | Last modified: | 2023-09-06 | Method: | X-RAY DIFFRACTION (1.5 Å) | Cite: | An isomorphous replacement method for efficient de novo phasing for serial femtosecond crystallography. Sci Rep, 5, 2015
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5D9C
| Luciferin-regenerating enzyme solved by SIRAS using XFEL (refined against Hg derivative data) | Descriptor: | (4S)-2-METHYL-2,4-PENTANEDIOL, Luciferin regenerating enzyme, MAGNESIUM ION, ... | Authors: | Yamashita, K, Pan, D, Okuda, T, Murai, T, Kodan, A, Yamaguchi, T, Gomi, K, Kajiyama, N, Kato, H, Ago, H, Yamamoto, M, Nakatsu, T. | Deposit date: | 2015-08-18 | Release date: | 2015-09-23 | Last modified: | 2023-09-06 | Method: | X-RAY DIFFRACTION (1.6 Å) | Cite: | An isomorphous replacement method for efficient de novo phasing for serial femtosecond crystallography. Sci Rep, 5, 2015
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