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Yorodumi- PDB-1hwy: BOVINE GLUTAMATE DEHYDROGENASE COMPLEXED WITH NAD AND 2-OXOGLUTARATE -
+Open data
-Basic information
Entry | Database: PDB / ID: 1hwy | ||||||
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Title | BOVINE GLUTAMATE DEHYDROGENASE COMPLEXED WITH NAD AND 2-OXOGLUTARATE | ||||||
Components | GLUTAMATE DEHYDROGENASE | ||||||
Keywords | OXIDOREDUCTASE / allostery / glutamate dehydrogenase / NAD | ||||||
Function / homology | Function and homology information glutamate dehydrogenase [NAD(P)+] activity / glutamate catabolic process / tricarboxylic acid metabolic process / glutamate dehydrogenase [NAD(P)+] / glutamate dehydrogenase (NADP+) activity / glutamate dehydrogenase (NAD+) activity / glutamine metabolic process / mitochondrial inner membrane / GTP binding / endoplasmic reticulum ...glutamate dehydrogenase [NAD(P)+] activity / glutamate catabolic process / tricarboxylic acid metabolic process / glutamate dehydrogenase [NAD(P)+] / glutamate dehydrogenase (NADP+) activity / glutamate dehydrogenase (NAD+) activity / glutamine metabolic process / mitochondrial inner membrane / GTP binding / endoplasmic reticulum / mitochondrion / ATP binding / identical protein binding Similarity search - Function | ||||||
Biological species | Bos taurus (cattle) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.2 Å | ||||||
Authors | Smith, T.J. / Peterson, P.E. / Schmidt, T. / Fang, J. / Stanley, C.A. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2001 Title: Structures of bovine glutamate dehydrogenase complexes elucidate the mechanism of purine regulation. Authors: Smith, T.J. / Peterson, P.E. / Schmidt, T. / Fang, J. / Stanley, C.A. #1: Journal: Structure / Year: 1999 Title: The Structure of Bovine Glutamate Dehydrogenase Provides Insights Into the Mechanism of Allostery Authors: Peterson, P.E. / Smith, T.J. #2: Journal: J.Struct.Biol. / Year: 1997 Title: Crystallization and Characterization of Bovine Liver Glutamate Dehydrogenase Authors: Peterson, P.E. / Pierce, J. / Smith, T.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1hwy.cif.gz | 578.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1hwy.ent.gz | 483.7 KB | Display | PDB format |
PDBx/mmJSON format | 1hwy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hw/1hwy ftp://data.pdbj.org/pub/pdb/validation_reports/hw/1hwy | HTTPS FTP |
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-Related structure data
Related structure data | 6dhdC 6dhqC 1hwx C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | Mass: 55638.211 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Cellular location: INNER MITOCHONDRIAL MATRIX / Organ: LIVER / Organelle: MITOCHONDRIAMitochondrion References: UniProt: P00366, glutamate dehydrogenase [NAD(P)+] #2: Chemical | ChemComp-PO4 / #3: Chemical | ChemComp-AKG / #4: Chemical | ChemComp-NAD / #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.98 Å3/Da / Density % sol: 58.73 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 Details: sodium phosphate, NaCl, PEG 8000, sodium azide, methyl pentanediol, octyl-b-glucopyranoside, pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 298K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 3→20 Å |
Reflection shell | Resolution: 3.2→3.4 Å / Rmerge(I) obs: 0.12 / % possible all: 78 |
Reflection | *PLUS % possible obs: 79 % / Rmerge(I) obs: 0.123 |
Reflection shell | *PLUS % possible obs: 80 % / Rmerge(I) obs: 0.475 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.2→8 Å / σ(F): 3 /
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Refinement step | Cycle: LAST / Resolution: 3.2→8 Å
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Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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