5XLF
 
 | | Crystal structure of aerobically purified and aerobically crystallized D. vulgaris Miyazaki F [NiFe]-hydrogenase | | Descriptor: | (4S)-2-METHYL-2,4-PENTANEDIOL, FE3-S4 CLUSTER, IRON/SULFUR CLUSTER, ... | | Authors: | Nishikawa, K, Mochida, S, Hiromoto, T, Shibata, N, Higuchi, Y. | | Deposit date: | 2017-05-10 | | Release date: | 2018-06-06 | | Method: | X-RAY DIFFRACTION (1.71 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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5XLG
 | | Crystal structure of anaerobically purified and aerobically crystallized D. vulgaris Miyazaki F [NiFe]-hydrogenase | | Descriptor: | (4S)-2-METHYL-2,4-PENTANEDIOL, 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL, FE3-S4 CLUSTER, ... | | Authors: | Nishikawa, K, Mochida, S, Hiromoto, T, Shibata, N, Higuchi, Y. | | Deposit date: | 2017-05-10 | | Release date: | 2018-06-06 | | Method: | X-RAY DIFFRACTION (1.64 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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5XLH
 | | Crystal structure of aerobically purified and aerobically crystallized for 12weeks D. vulgaris Miyazaki F [NiFe]-hydrogenase | | Descriptor: | (4S)-2-METHYL-2,4-PENTANEDIOL, FE3-S4 CLUSTER, IRON/SULFUR CLUSTER, ... | | Authors: | Nishikawa, K, Mochida, S, Hiromoto, T, Shibata, N, Higuchi, Y. | | Deposit date: | 2017-05-10 | | Release date: | 2018-06-06 | | Method: | X-RAY DIFFRACTION (1.93 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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5XLE
 | | Crystal structure of anaerobically purified and anaerobically crystallized D. vulgaris Miyazaki F [NiFe]-hydrogenase | | Descriptor: | (4S)-2-METHYL-2,4-PENTANEDIOL, 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL, FE3-S4 CLUSTER, ... | | Authors: | Nishikawa, K, Mochida, S, Hiromoto, T, Shibata, N, Higuchi, Y. | | Deposit date: | 2017-05-10 | | Release date: | 2018-06-06 | | Last modified: | 2024-03-27 | | 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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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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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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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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1WQ5
 | | Crystal structure of tryptophan synthase alpha-subunit from Escherichia coli | | Descriptor: | GLYCEROL, SULFATE ION, Tryptophan synthase alpha chain | | Authors: | Nishio, K, Morimoto, Y, Ishizuka, M, Ogasahara, K, Yutani, K, Tsukihara, T, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | | Deposit date: | 2004-09-22 | | Release date: | 2005-02-15 | | Last modified: | 2024-04-03 | | Method: | X-RAY DIFFRACTION (2.3 Å) | | Cite: | Conformational Changes in the alpha-Subunit Coupled to Binding of the beta(2)-Subunit of Tryptophan Synthase from Escherichia coli: Crystal Structure of the Tryptophan Synthase alpha-Subunit Alon
Biochemistry, 44, 2005
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1V7Y
 | | Crystal structure of tryptophan synthase alpha-subunit from Escherichia coli at room temperature | | Descriptor: | SULFATE ION, Tryptophan synthase alpha chain | | Authors: | Nishio, K, Morimoto, Y, Ishizuka, M, Ogasahara, K, Yutani, K, Tsukihara, T, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | | Deposit date: | 2003-12-25 | | Release date: | 2005-02-15 | | Last modified: | 2023-12-27 | | Method: | X-RAY DIFFRACTION (2.5 Å) | | Cite: | Conformational Changes in the alpha-Subunit Coupled to Binding of the beta(2)-Subunit of Tryptophan Synthase from Escherichia coli: Crystal Structure of the Tryptophan Synthase alpha-Subunit Alon
Biochemistry, 44, 2005
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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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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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5EJN
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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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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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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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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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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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4HPC
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4HPB
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4HPD
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4HPA
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4YNX
 | | Structure of YdiE from E. coli | | Descriptor: | SULFATE ION, Uncharacterized protein YdiE | | Authors: | Tame, J.R.H, Nishimura, K, Zhang, K.Y.J. | | Deposit date: | 2015-03-11 | | Release date: | 2015-05-20 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (1.5 Å) | | Cite: | The crystal and solution structure of YdiE from Escherichia coli
Acta Crystallogr.,Sect.F, 71, 2015
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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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