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Yorodumi- PDB-1euz: GLUTAMATE DEHYDROGENASE FROM THERMOCOCCUS PROFUNDUS IN THE UNLIGA... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1euz | ||||||
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Title | GLUTAMATE DEHYDROGENASE FROM THERMOCOCCUS PROFUNDUS IN THE UNLIGATED STATE | ||||||
Components | GLUTAMATE DEHYDROGENASE | ||||||
Keywords | OXIDOREDUCTASE / GLUTAMATE / HYPERTHERMOSTABILITY / domain closure movement | ||||||
Function / homology | Function and homology information glutamate dehydrogenase [NAD(P)+] / glutamate dehydrogenase (NADP+) activity / glutamate dehydrogenase (NAD+) activity / amino acid metabolic process Similarity search - Function | ||||||
Biological species | Thermococcus profundus (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å | ||||||
Authors | Nakasako, M. | ||||||
Citation | Journal: Biochemistry / Year: 2001 Title: Large-scale domain movements and hydration structure changes in the active-site cleft of unligated glutamate dehydrogenase from Thermococcus profundus studied by cryogenic X-ray crystal ...Title: Large-scale domain movements and hydration structure changes in the active-site cleft of unligated glutamate dehydrogenase from Thermococcus profundus studied by cryogenic X-ray crystal structure analysis and small-angle X-ray scattering. Authors: Nakasako, M. / Fujisawa, T. / Adachi, S. / Kudo, T. / Higuchi, S. #1: Journal: Acta Crystallogr.,Sect.D / Year: 1999 Title: Crystallization and Preliminary X-ray Diffraction Studies of Hyperthermostable Glutamate Dehydrogenase from Thermococcus profundus Authors: Higuchi, S. / Nakasako, M. / Kudo, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1euz.cif.gz | 468.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1euz.ent.gz | 390.2 KB | Display | PDB format |
PDBx/mmJSON format | 1euz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/eu/1euz ftp://data.pdbj.org/pub/pdb/validation_reports/eu/1euz | HTTPS FTP |
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-Related structure data
Related structure data | |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 46758.477 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermococcus profundus (archaea) / Production host: Escherichia coli (E. coli) / References: UniProt: O74024, glutamate dehydrogenase #2: Chemical | ChemComp-SO4 / |
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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: 3.97 Å3/Da / Density % sol: 69.03 % Description: DATA WERE COLLECTED USING THE OSCILLATION METHOD | |||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5 Details: PEG8000, Lithium sulfate, sodium acetate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K | |||||||||||||||||||||||||
Crystal grow | *PLUS | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL44B2 / Wavelength: 1 |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Mar 15, 1999 / Details: PT-COATED CYLINDRICAL BENT MIRROR |
Radiation | Monochromator: FIXED EXIT DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.25→100 Å / Num. all: 206382 / Num. obs: 206382 / % possible obs: 99.7 % / Observed criterion σ(F): 1488939 / Observed criterion σ(I): 1 / Redundancy: 7.21 % / Rmerge(I) obs: 0.072 / Net I/σ(I): 17.9 |
Reflection shell | Resolution: 2.25→2.33 Å / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 3.4 / % possible all: 99.4 |
Reflection | *PLUS Num. measured all: 1488939 / Rmerge(I) obs: 0.063 |
Reflection shell | *PLUS % possible obs: 99.4 % / Rmerge(I) obs: 0.322 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.25→8 Å / Data cutoff high absF: 100000 / Data cutoff low absF: 1 / Isotropic thermal model: GAUSS / σ(F): 2 / Stereochemistry target values: Engh & Huber
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Refine analyze | Luzzati coordinate error obs: 0.25 Å | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.25→8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.25→2.35 Å
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Software | *PLUS Name: X-PLOR / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS Rfactor Rwork: 0.188 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS |