1NYJ
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5Y4N
| Crystal structure of aerobically purified and anaerobically crystallized D. vulgaris Miyazaki F [NiFe]-hydrogenase | Descriptor: | (4R)-2-METHYLPENTANE-2,4-DIOL, (4S)-2-METHYL-2,4-PENTANEDIOL, 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL, ... | Authors: | Nishikawa, K, Mochida, S, Hiromoto, T, Shibata, N, Higuchi, Y. | Deposit date: | 2017-08-04 | Release date: | 2018-08-08 | Last modified: | 2020-02-19 | Method: | X-RAY DIFFRACTION (1.69 Å) | Cite: | Ni-elimination from the active site of the standard [NiFe]‐hydrogenase upon oxidation by O2. J.Inorg.Biochem., 177, 2017
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3A7S
| Catalytic domain of UCH37 | Descriptor: | CHLORIDE ION, Ubiquitin carboxyl-terminal hydrolase isozyme L5 | Authors: | Nishio, K, Kim, S.W, Kawai, K, Mizushima, T, Yamane, T, Hamazaki, J, Murata, S, Tanaka, K. | Deposit date: | 2009-10-04 | Release date: | 2009-11-03 | Last modified: | 2024-05-29 | Method: | X-RAY DIFFRACTION (2.2 Å) | Cite: | Crystal structure of the de-ubiquitinating enzyme UCH37 (human UCH-L5) catalytic domain Biochem.Biophys.Res.Commun., 2009
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1WY5
| Crystal structure of isoluecyl-tRNA lysidine synthetase | Descriptor: | Hypothetical UPF0072 protein AQ_1887 | Authors: | Nakanishi, K, Fukai, S, Ikeuchi, Y, Soma, A, Sekine, Y, Suzuki, T, Nureki, O, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | Deposit date: | 2005-02-06 | Release date: | 2005-05-03 | Last modified: | 2024-03-13 | Method: | X-RAY DIFFRACTION (2.42 Å) | Cite: | Structural basis for lysidine formation by ATP pyrophosphatase accompanied by a lysine-specific loop and a tRNA-recognition domain. Proc.Natl.Acad.Sci.Usa, 102, 2005
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6IW3
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6K5V
| Structure of CSY4 Apo-form | Descriptor: | CHLORIDE ION, Citrate synthase 4, mitochondrial | Authors: | Nishio, K, Mizushima, T. | Deposit date: | 2019-05-31 | Release date: | 2020-03-18 | Last modified: | 2023-11-22 | Method: | X-RAY DIFFRACTION (2.69 Å) | Cite: | Structural and biochemical characterization of mitochondrial citrate synthase 4 from Arabidopsis thaliana. Acta Crystallogr.,Sect.F, 76, 2020
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6JCK
| Complex structure of Axin-DIX and Dvl2-DIX | Descriptor: | Axin-1, Segment polarity protein dishevelled homolog DVL-2 | Authors: | Yamanishi, K, Shibata, N. | Deposit date: | 2019-01-29 | Release date: | 2020-01-15 | Last modified: | 2023-11-22 | Method: | X-RAY DIFFRACTION (3.09 Å) | Cite: | A direct heterotypic interaction between the DIX domains of Dishevelled and Axin mediates signaling to beta-catenin. Sci.Signal., 12, 2019
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2DH6
| Crystal structure of E. coli Apo-TrpB | Descriptor: | SULFATE ION, tryptophan synthase beta subunit | Authors: | Nishio, K, Morimoto, Y, Ogasahara, K, Yasuoka, N, Yutani, K, Tsukihara, T, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | Deposit date: | 2006-03-23 | Release date: | 2007-04-24 | Last modified: | 2023-10-25 | Method: | X-RAY DIFFRACTION (3 Å) | Cite: | Large conformational changes in the Escherichia coli tryptophan synthase beta(2) subunit upon pyridoxal 5'-phosphate binding Febs J., 277, 2010
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2DH5
| Crystal structure of E. coli Holo-TrpB | Descriptor: | GLYCEROL, PYRIDOXAL-5'-PHOSPHATE, SULFATE ION, ... | Authors: | Nishio, K, Morimoto, Y, Ogasahara, K, Yutani, K, Tsukihara, T, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | Deposit date: | 2006-03-23 | Release date: | 2007-04-24 | Last modified: | 2023-10-25 | Method: | X-RAY DIFFRACTION (2.9 Å) | Cite: | Large conformational changes in the Escherichia coli tryptophan synthase beta(2) subunit upon pyridoxal 5'-phosphate binding Febs J., 277, 2010
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3AK5
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3A2K
| Crystal structure of TilS complexed with tRNA | Descriptor: | bacterial tRNA, tRNA(Ile)-lysidine synthase | Authors: | Nakanishi, K, Bonnefond, L, Ishitani, R, Nureki, O. | Deposit date: | 2009-05-23 | Release date: | 2009-10-20 | Last modified: | 2018-01-24 | Method: | X-RAY DIFFRACTION (3.65 Å) | Cite: | Structural basis for translational fidelity ensured by transfer RNA lysidine synthetase. Nature, 461, 2009
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2CSX
| Crystal structure of Aquifex aeolicus methionyl-tRNA synthetase complexed with tRNA(Met) | Descriptor: | Methionyl-tRNA synthetase, RNA (75-MER) | Authors: | Nakanishi, K, Ogiso, Y, Nakama, T, Fukai, S, Nureki, O, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | Deposit date: | 2005-05-23 | Release date: | 2005-09-20 | Last modified: | 2024-03-13 | Method: | X-RAY DIFFRACTION (2.7 Å) | Cite: | Structural basis for anticodon recognition by methionyl-tRNA synthetase. Nat.Struct.Mol.Biol., 12, 2005
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2CT8
| Crystal structure of Aquifex aeolicus methionyl-tRNA synthetase complexed with tRNA(Met) and methionyl-adenylate anologue | Descriptor: | 5'-O-[(L-METHIONYL)-SULPHAMOYL]ADENOSINE, Methionyl-tRNA synthetase, RNA (74-MER) | Authors: | Nakanishi, K, Ogiso, Y, Nakama, T, Fukai, S, Nureki, O, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | Deposit date: | 2005-05-23 | Release date: | 2005-09-20 | Last modified: | 2024-03-13 | Method: | X-RAY DIFFRACTION (2.7 Å) | Cite: | Structural basis for anticodon recognition by methionyl-tRNA synthetase. Nat.Struct.Mol.Biol., 12, 2005
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7VXQ
| The Carbon Monoxide Complex of [NiFe]-hydrogenase (Hyb-type) from Citrobacter sp. S-77 | Descriptor: | CARBON MONOXIDE, FE3-S4 CLUSTER, GLYCEROL, ... | Authors: | Nishikawa, K, Higuchi, K, Imanishi, T, Higuchi, Y. | Deposit date: | 2021-11-13 | Release date: | 2022-02-09 | Last modified: | 2023-11-29 | Method: | X-RAY DIFFRACTION (1.77 Å) | Cite: | Structural and spectroscopic characterization of CO inhibition of [NiFe]-hydrogenase from Citrobacter sp. S-77. Acta Crystallogr.,Sect.F, 78, 2022
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5XVC
| [NiFe]-hydrogenase (Hyb-type) from Citrobacter sp. S-77 in a ferricyanide-oxidized condition | Descriptor: | DI(HYDROXYETHYL)ETHER, FE3-S4 CLUSTER, FE4-S4-O CLUSTER, ... | Authors: | Nishikawa, K, Matsuura, H, Muhd Noor, N.D, Tai, H, Hirota, S, Kim, J, Kang, J, Tateno, M, Yoon, K.S, Ogo, S, Shomura, Y, Higuchi, Y. | Deposit date: | 2017-06-27 | Release date: | 2018-06-27 | Last modified: | 2019-07-10 | Method: | X-RAY DIFFRACTION (2.05 Å) | Cite: | Redox-dependent conformational changes of a proximal [4Fe-4S] cluster in Hyb-type [NiFe]-hydrogenase to protect the active site from O2. Chem.Commun.(Camb.), 54, 2018
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5XVD
| [NiFe]-hydrogenase (Hyb-type) from Citrobacter sp. S-77 in an air-oxidized condition | Descriptor: | FE3-S4 CLUSTER, FE4-S4-O CLUSTER, GLYCEROL, ... | Authors: | Nishikawa, K, Matsuura, H, Muhd Noor, N.D, Tai, H, Hirota, S, Kim, J, Kang, J, Tateno, M, Yoon, K.S, Ogo, S, Shomura, Y, Higuchi, Y. | Deposit date: | 2017-06-27 | Release date: | 2018-06-27 | Last modified: | 2019-07-10 | Method: | X-RAY DIFFRACTION (1.57 Å) | Cite: | Redox-dependent conformational changes of a proximal [4Fe-4S] cluster in Hyb-type [NiFe]-hydrogenase to protect the active site from O2. Chem.Commun.(Camb.), 54, 2018
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5XVB
| [NiFe]-hydrogenase (Hyb-type) from Citrobacter sp. S-77 in an H2-reduced condition | Descriptor: | FE3-S4 CLUSTER, GLYCEROL, IRON/SULFUR CLUSTER, ... | Authors: | Nishikawa, K, Matsuura, H, Muhd Noor, N.D, Tai, H, Hirota, S, Kim, J, Kang, J, Tateno, M, Yoon, K.S, Ogo, S, Shomura, Y, Higuchi, Y. | Deposit date: | 2017-06-27 | Release date: | 2018-06-27 | Last modified: | 2024-03-27 | Method: | X-RAY DIFFRACTION (1.84 Å) | Cite: | Redox-dependent conformational changes of a proximal [4Fe-4S] cluster in Hyb-type [NiFe]-hydrogenase to protect the active site from O2. Chem.Commun.(Camb.), 54, 2018
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5BUP
| Crystal structure of the ZP-C domain of mouse ZP2 | Descriptor: | ACETATE ION, Zona pellucida sperm-binding protein 2 | Authors: | Nishimura, K, Jovine, L. | Deposit date: | 2015-06-04 | Release date: | 2016-01-27 | Last modified: | 2017-09-06 | Method: | X-RAY DIFFRACTION (2.251 Å) | Cite: | A structured interdomain linker directs self-polymerization of human uromodulin. Proc.Natl.Acad.Sci.USA, 113, 2016
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3RV1
| Crystal structure of the N-terminal and RNase III domains of K. polysporus Dcr1 E224Q mutant | Descriptor: | K. polysporus Dcr1 | Authors: | Nakanishi, K, Weinberg, D.E, Bartel, D.P, Patel, D.J. | Deposit date: | 2011-05-05 | Release date: | 2011-08-03 | Last modified: | 2024-02-28 | Method: | X-RAY DIFFRACTION (1.975 Å) | Cite: | The inside-out mechanism of dicers from budding yeasts. Cell(Cambridge,Mass.), 146, 2011
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3RV0
| Crystal structure of K. polysporus Dcr1 without the C-terminal dsRBD | Descriptor: | K. polysporus Dcr1, MAGNESIUM ION | Authors: | Nakanishi, K, Weinberg, D.E, Bartel, D.P, Patel, D.J. | Deposit date: | 2011-05-05 | Release date: | 2011-08-03 | Last modified: | 2024-02-28 | Method: | X-RAY DIFFRACTION (2.29 Å) | Cite: | The inside-out mechanism of dicers from budding yeasts. Cell(Cambridge,Mass.), 146, 2011
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5EJN
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5H6U
| Structure of alginate-binding protein AlgQ2 in complex with an alginate pentasaccharide | Descriptor: | AlgQ2, CALCIUM ION, beta-D-mannopyranuronic acid-(1-4)-beta-D-mannopyranuronic acid-(1-4)-beta-D-mannopyranuronic acid-(1-4)-beta-D-mannopyranuronic acid-(1-4)-beta-D-mannopyranuronic acid | Authors: | Uenishi, K, Kaneko, A, Maruyama, Y, Mikami, B, Murata, K, Hashimoto, W. | Deposit date: | 2016-11-15 | Release date: | 2017-08-09 | Last modified: | 2023-11-08 | Method: | X-RAY DIFFRACTION (2.006 Å) | Cite: | A solute-binding protein in the closed conformation induces ATP hydrolysis in a bacterial ATP-binding cassette transporter involved in the import of alginate J. Biol. Chem., 292, 2017
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5MR3
| Crystal structure of red abalone egg VERL repeat 2 with linker in complex with sperm lysin at 1.8 A resolution | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose, CHLORIDE ION, Egg-lysin, ... | Authors: | Nishimura, K, Raj, I, Sadat Al-Hosseini, H, De Sanctis, D, Jovine, L. | Deposit date: | 2016-12-21 | Release date: | 2017-06-14 | Last modified: | 2024-01-17 | Method: | X-RAY DIFFRACTION (1.8 Å) | Cite: | Structural Basis of Egg Coat-Sperm Recognition at Fertilization. Cell, 169, 2017
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5H71
| Structure of alginate-binding protein AlgQ2 in complex with an alginate trisaccharide | Descriptor: | 4-deoxy-alpha-L-erythro-hex-4-enopyranuronic acid-(1-4)-beta-D-mannopyranuronic acid-(1-4)-beta-D-mannopyranuronic acid, AlgQ2, CALCIUM ION, ... | Authors: | Uenishi, K, Kaneko, A, Maruyama, Y, Mikami, B, Murata, K, Hashimoto, W. | Deposit date: | 2016-11-15 | Release date: | 2017-08-09 | Last modified: | 2023-11-08 | Method: | X-RAY DIFFRACTION (1.549 Å) | Cite: | A solute-binding protein in the closed conformation induces ATP hydrolysis in a bacterial ATP-binding cassette transporter involved in the import of alginate J. Biol. Chem., 292, 2017
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4HPA
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