5B0P
 
 | | Beta-1,2-Mannobiose phosphorylase from Listeria innocua - glycerol complex | | Descriptor: | 2-(N-MORPHOLINO)-ETHANESULFONIC ACID, GLYCEROL, Lin0857 protein, ... | | Authors: | Tsuda, T, Arakawa, T, Fushinobu, S. | | Deposit date: | 2015-11-02 | | Release date: | 2015-12-02 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (1.9 Å) | | Cite: | Characterization and crystal structure determination of beta-1,2-mannobiose phosphorylase from Listeria innocua
Febs Lett., 589, 2015
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5B0S
 | | Beta-1,2-Mannobiose phosphorylase from Listeria innocua - beta-1,2-mannotriose complex | | Descriptor: | 2-(N-MORPHOLINO)-ETHANESULFONIC ACID, GLYCEROL, Lin0857 protein, ... | | Authors: | Tsuda, T, Arakawa, T, Fushinobu, S. | | Deposit date: | 2015-11-02 | | Release date: | 2015-12-02 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (2.1 Å) | | Cite: | Characterization and crystal structure determination of beta-1,2-mannobiose phosphorylase from Listeria innocua
Febs Lett., 589, 2015
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5B0R
 | | Beta-1,2-Mannobiose phosphorylase from Listeria innocua - beta-1,2-mannobiose complex | | Descriptor: | 2-(N-MORPHOLINO)-ETHANESULFONIC ACID, GLYCEROL, Lin0857 protein, ... | | Authors: | Tsuda, T, Arakawa, T, Fushinobu, S. | | Deposit date: | 2015-11-02 | | Release date: | 2015-12-02 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (1.8 Å) | | Cite: | Characterization and crystal structure determination of beta-1,2-mannobiose phosphorylase from Listeria innocua
Febs Lett., 589, 2015
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5B0Q
 | | beta-1,2-Mannobiose phosphorylase from Listeria innocua - mannose complex | | Descriptor: | 2-(N-MORPHOLINO)-ETHANESULFONIC ACID, Lin0857 protein, SULFATE ION, ... | | Authors: | Tsuda, T, Arakawa, T, Fushinobu, S. | | Deposit date: | 2015-11-02 | | Release date: | 2015-12-02 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (2.3 Å) | | Cite: | Characterization and crystal structure determination of beta-1,2-mannobiose phosphorylase from Listeria innocua
Febs Lett., 589, 2015
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3WNZ
 | | Crystal structure of Bacillus subtilis YwfE, an L-amino acid ligase, with bound ADP-Mg-Pi | | Descriptor: | ADENOSINE-5'-DIPHOSPHATE, Alanine-anticapsin ligase BacD, MAGNESIUM ION, ... | | Authors: | Tsuda, T, Kojima, S. | | Deposit date: | 2013-12-19 | | Release date: | 2014-05-14 | | Last modified: | 2024-03-20 | | Method: | X-RAY DIFFRACTION (1.9 Å) | | Cite: | Single Mutation Alters the Substrate Specificity of l-Amino Acid Ligase
Biochemistry, 53, 2014
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3WO0
 | | Crystal structure of Bacillus subtilis YwfE, an L-amino acid ligase, with bound ADP-Mg-Ala | | Descriptor: | ADENOSINE-5'-DIPHOSPHATE, ALANINE, Alanine-anticapsin ligase BacD, ... | | Authors: | Tsuda, T, Kojima, S. | | Deposit date: | 2013-12-19 | | Release date: | 2014-05-14 | | Last modified: | 2024-03-20 | | Method: | X-RAY DIFFRACTION (2 Å) | | Cite: | Single Mutation Alters the Substrate Specificity of l-Amino Acid Ligase
Biochemistry, 53, 2014
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3WO1
 | | Crystal structure of Trp332Ala mutant YwfE, an L-amino acid ligase, with bound ADP-Mg-Ala | | Descriptor: | ADENOSINE-5'-DIPHOSPHATE, ALANINE, Alanine-anticapsin ligase BacD, ... | | Authors: | Tsuda, T, Kojima, S. | | Deposit date: | 2013-12-19 | | Release date: | 2014-05-14 | | Last modified: | 2024-03-20 | | Method: | X-RAY DIFFRACTION (2.3 Å) | | Cite: | Single Mutation Alters the Substrate Specificity of l-Amino Acid Ligase
Biochemistry, 53, 2014
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3A1E
 | | Crystal structure of the P- and N-domains of His462Gln mutant CopA, a copper-transporting P-type ATPase, bound with AMPPCP-Mg | | Descriptor: | MAGNESIUM ION, PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER, Probable copper-exporting P-type ATPase A | | Authors: | Tsuda, T, Toyoshima, C. | | Deposit date: | 2009-03-31 | | Release date: | 2009-07-21 | | Last modified: | 2023-11-01 | | Method: | X-RAY DIFFRACTION (1.95 Å) | | Cite: | Nucleotide recognition by CopA, a Cu+-transporting P-type ATPase.
Embo J., 28, 2009
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3A1C
 | | crystal structure of the P- and N-domains of CopA, a copper-transporting P-type ATPase, bound with AMPPCP-Mg | | Descriptor: | MAGNESIUM ION, PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER, Probable copper-exporting P-type ATPase A | | Authors: | Tsuda, T, Toyoshima, C. | | Deposit date: | 2009-03-31 | | Release date: | 2009-07-21 | | Last modified: | 2023-11-01 | | Method: | X-RAY DIFFRACTION (1.85 Å) | | Cite: | Nucleotide recognition by CopA, a Cu+-transporting P-type ATPase.
Embo J., 28, 2009
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3A1D
 | | Crystal structure of the P- and N-domains of CopA, a copper-transporting P-type ATPase, bound with ADP-Mg | | Descriptor: | ADENOSINE-5'-DIPHOSPHATE, MAGNESIUM ION, Probable copper-exporting P-type ATPase A | | Authors: | Tsuda, T, Toyoshima, C. | | Deposit date: | 2009-03-31 | | Release date: | 2009-07-21 | | Last modified: | 2023-11-01 | | Method: | X-RAY DIFFRACTION (1.85 Å) | | Cite: | Nucleotide recognition by CopA, a Cu+-transporting P-type ATPase.
Embo J., 28, 2009
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5XWD
 | | Crystal structure of the complex of 059-152-Fv and EGFR-ECD | | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Epidermal growth factor receptor, ... | | Authors: | Matsuda, T, Ito, T, Shirouzu, M. | | Deposit date: | 2017-06-29 | | Release date: | 2018-02-28 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (2.894 Å) | | Cite: | Cell-free synthesis of functional antibody fragments to provide a structural basis for antibody-antigen interaction
PLoS ONE, 13, 2018
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5YE4
 | | Crystal structure of the complex of di-acetylated histone H4 and 1A9D7 Fab fragment | | Descriptor: | 1A9D7 L chain, 1A9D7 VH CH1 chain, ZINC ION, ... | | Authors: | Matsuda, T, Ito, T, Wakamori, M, Umehara, T. | | Deposit date: | 2017-09-15 | | Release date: | 2018-08-22 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (1.799 Å) | | Cite: | JQ1 affects BRD2-dependent and independent transcription regulation without disrupting H4-hyperacetylated chromatin states.
Epigenetics, 13, 2018
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5YE3
 | | Crystal structure of the complex of di-acetylated histone H4 and 2A7D9 Fab fragment | | Descriptor: | 2A7D9 L chain, 2A7D9 VH CH1 chain, di-acetylated histone H4 | | Authors: | Matsuda, T, Ito, T, Wakamori, M, Umehara, T. | | Deposit date: | 2017-09-15 | | Release date: | 2018-08-22 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (1.7 Å) | | Cite: | JQ1 affects BRD2-dependent and independent transcription regulation without disrupting H4-hyperacetylated chromatin states.
Epigenetics, 13, 2018
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1WPG
 | | Crystal structure of the SR CA2+-ATPase with MGF4 | | Descriptor: | ADENOSINE-5'-DIPHOSPHATE, MAGNESIUM ION, OCTANOIC ACID [3S-[3ALPHA, ... | | Authors: | Toyoshima, C, Nomura, H, Tsuda, T. | | Deposit date: | 2004-09-02 | | Release date: | 2004-10-05 | | Last modified: | 2024-04-03 | | Method: | X-RAY DIFFRACTION (2.3 Å) | | Cite: | Lumenal gating mechanism revealed in calcium pump crystal structures with phosphate analogues
Nature, 432, 2004
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2ZBD
 | | Crystal Structure of the SR Calcium Pump with Bound Aluminium Fluoride, ADP and Calcium | | Descriptor: | 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE, ADENOSINE-5'-DIPHOSPHATE, CALCIUM ION, ... | | Authors: | Toyoshima, C, Nomura, H, Tsuda, T, Ogawa, H, Norimatsu, Y. | | Deposit date: | 2007-10-20 | | Release date: | 2007-11-20 | | Last modified: | 2023-11-01 | | Method: | X-RAY DIFFRACTION (2.4 Å) | | Cite: | Lumenal gating mechanism revealed in calcium pump crystal structures with phosphate analogues
Nature, 432, 2004
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2FYH
 | | Solution structure of the 2'-5' RNA ligase-like protein from Pyrococcus furiosus | | Descriptor: | putative integral membrane transport protein | | Authors: | Okada, K, Matsuda, T, Sakamoto, T, Muto, Y, Yokoyama, S, Kanai, A, Kawai, G, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | | Deposit date: | 2006-02-08 | | Release date: | 2007-02-20 | | Last modified: | 2024-05-01 | | Method: | SOLUTION NMR | | Cite: | Characterization of a heat-stable enzyme possessing GTP-dependent RNA ligase activity from a hyperthermophilic archaeon, Pyrococcus furiosus
Rna, 15, 2009
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1V9J
 | | Solution structure of a BolA-like protein from Mus musculus | | Descriptor: | BolA-like protein RIKEN cDNA 1110025L05 | | Authors: | Kasai, T, Inoue, M, Koshiba, S, Yabuki, T, Aoki, M, Nunokawa, E, Seki, E, Matsuda, T, Matsuda, N, Tomo, Y, Shirouzu, M, Terada, T, Obayashi, N, Hamana, H, Shinya, N, Tatsuguchi, A, Yasuda, S, Yoshida, M, Hirota, H, Matsuo, Y, Tani, K, Suzuki, H, Arakawa, T, Carninci, P, Kawai, J, Hayashizaki, Y, Kigawa, T, Yokoyama, S, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | | Deposit date: | 2004-01-26 | | Release date: | 2004-02-10 | | Last modified: | 2023-12-27 | | Method: | SOLUTION NMR | | Cite: | Solution structure of a BolA-like protein from Mus musculus
Protein Sci., 13, 2004
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1IOZ
 | | Crystal Structure of the C-HA-RAS Protein Prepared by the Cell-Free Synthesis | | Descriptor: | GUANOSINE-5'-DIPHOSPHATE, TRANSFORMING PROTEIN P21/H-RAS-1 | | Authors: | Kigawa, T, Yamaguchi-Nunokawa, E, Kodama, K, Matsuda, T, Yabuki, T, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | | Deposit date: | 2001-04-18 | | Release date: | 2001-10-03 | | Last modified: | 2023-12-27 | | Method: | X-RAY DIFFRACTION (2 Å) | | Cite: | Selenomethionine incorporation into a protein by cell-free synthesis
J.STRUCT.FUNCT.GENOM., 2, 2001
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3UFZ
 | | Crystal structure of a Trp-less green fluorescent protein translated by the universal genetic code | | Descriptor: | Green fluorescent protein | | Authors: | Kawahara-Kobayashi, A, Araiso, Y, Matsuda, T, Yokoyama, S, Kigawa, T, Nureki, O, Kiga, D. | | Deposit date: | 2011-11-02 | | Release date: | 2012-10-17 | | Last modified: | 2023-12-06 | | Method: | X-RAY DIFFRACTION (1.85 Å) | | Cite: | Simplification of the genetic code: restricted diversity of genetically encoded amino acids.
Nucleic Acids Res., 40, 2012
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3UG0
 | | Crystal structure of a Trp-less green fluorescent protein translated by the simplified genetic code | | Descriptor: | Green fluorescent protein | | Authors: | Kawahara-Kobayashi, A, Araiso, Y, Matsuda, T, Yokoyama, S, Kigawa, T, Nureki, O, Kiga, D. | | Deposit date: | 2011-11-02 | | Release date: | 2012-10-17 | | Last modified: | 2023-12-06 | | Method: | X-RAY DIFFRACTION (2.093 Å) | | Cite: | Simplification of the genetic code: restricted diversity of genetically encoded amino acids.
Nucleic Acids Res., 40, 2012
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1VDY
 | | NMR Structure of the hypothetical ENTH-VHS domain At3g16270 from Arabidopsis thaliana | | Descriptor: | hypothetical protein (RAFL09-17-B18) | | Authors: | Lopez-Mendez, B, Pantoja-Uceda, D, Tomizawa, T, Koshiba, S, Kigawa, T, Shirouzu, M, Terada, T, Inoue, M, Yabuki, T, Aoki, M, Seki, E, Matsuda, T, Hirota, H, Yoshida, M, Tanaka, A, Osanai, T, Seki, M, Shinozaki, K, Yokoyama, S, Guntert, P, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | | Deposit date: | 2004-03-25 | | Release date: | 2005-05-03 | | Last modified: | 2023-12-27 | | Method: | SOLUTION NMR | | Cite: | Solution structure of the hypothetical ENTH-VHS domain AT3G16270 from arabidopsis thaliana
To be Published
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2UXS
 | | 2.7A crystal structure of inorganic pyrophosphatase (Rv3628) from Mycobacterium tuberculosis at pH 7.5 | | Descriptor: | INORGANIC PYROPHOSPHATASE, PHOSPHATE ION | | Authors: | Cole, R.E, Cianci, M, Hall, J.F, Matsuda, T, Kigawa, T, Yokoyama, S, Hasnain, S.S, Tabernero, L. | | Deposit date: | 2007-03-29 | | Release date: | 2008-05-27 | | Last modified: | 2023-12-13 | | Method: | X-RAY DIFFRACTION (2.7 Å) | | Cite: | Crystal Structure of Rv3628: An Inorganic Pyrophosphatase from Mycobacterium Tuberculosis
To be Published
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1UGK
 | | Solution structure of the first C2 domain of synaptotagmin IV from human fetal brain (KIAA1342) | | Descriptor: | Synaptotagmin IV | | Authors: | Nagashima, T, Hayashi, F, Shirouzu, M, Terada, T, Kigawa, T, Inoue, M, Yabuki, T, Aoki, M, Seki, E, Matsuda, T, Hirota, H, Yoshida, M, Tanaka, A, Osanai, T, Matsuo, Y, Ohara, O, Nagase, T, Kikuno, R, Nakayama, M, Yokoyama, S, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | | Deposit date: | 2003-06-16 | | Release date: | 2003-12-16 | | Last modified: | 2023-12-27 | | Method: | SOLUTION NMR | | Cite: | Solution structure of the first C2 domain of synaptotagmin IV from human fetal brain (KIAA1342)
To be Published
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1UG8
 | | NMR structure of the R3H domain from Poly(A)-specific Ribonuclease | | Descriptor: | Poly(A)-specific Ribonuclease | | Authors: | Nagata, T, Muto, Y, Hayami, N, Uda, H, Shirouzu, M, Terada, T, Kigawa, T, Inoue, M, Yabuki, T, Aoki, M, Seki, E, Matsuda, T, Hirota, H, Yoshida, M, Kobayashi, N, Tanaka, A, Osanai, T, Matsuo, Y, Arakawa, T, Carninci, P, Kawai, J, Hayashizaki, Y, Yokoyama, S, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | | Deposit date: | 2003-06-15 | | Release date: | 2004-08-17 | | Last modified: | 2023-12-27 | | Method: | SOLUTION NMR | | Cite: | NMR structure of the R3H domain from Poly(A)-specific Ribonuclease
To be Published
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1UG1
 | | SH3 domain of Hypothetical protein BAA76854.1 | | Descriptor: | KIAA1010 protein | | Authors: | Nagata, T, Muto, Y, Kamewari, Y, Shirouzu, M, Terada, T, Kigawa, T, Inoue, M, Yabuki, T, Aoki, M, Seki, E, Matsuda, T, Hirota, H, Yoshida, M, Kobayashi, N, Tanaka, A, Osanai, T, Matsuo, Y, Ohara, O, Nagase, T, Kikuno, R, Nakayama, M, Yokoyama, S, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | | Deposit date: | 2003-06-11 | | Release date: | 2003-12-11 | | Last modified: | 2023-12-27 | | Method: | SOLUTION NMR | | Cite: | NMR structure of SH3 domain of Hypothetical protein BAA76854.1
To be Published
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