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Yorodumi- PDB-8zmu: GLUTAMATE DEHYDROGENASE (W89F-MUTANT) FROM THERMOCOCCUS PROFUNDUS... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8zmu | ||||||||||||||||||||||||||||||||||||||||||
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Title | GLUTAMATE DEHYDROGENASE (W89F-MUTANT) FROM THERMOCOCCUS PROFUNDUS IN THE UNLIGANDED STATE | ||||||||||||||||||||||||||||||||||||||||||
Components | Glutamate dehydrogenase | ||||||||||||||||||||||||||||||||||||||||||
Keywords | OXIDOREDUCTASE | ||||||||||||||||||||||||||||||||||||||||||
Function / homology | Function and homology information glutamate dehydrogenase [NAD(P)+] / glutamate dehydrogenase (NADP+) activity / glutamate dehydrogenase (NAD+) activity / glutamate catabolic process Similarity search - Function | ||||||||||||||||||||||||||||||||||||||||||
Biological species | Thermococcus profundus (archaea) | ||||||||||||||||||||||||||||||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.028 Å | ||||||||||||||||||||||||||||||||||||||||||
Authors | Wakabayashi, T. / Matsui, Y. / Masayoshi, M. | ||||||||||||||||||||||||||||||||||||||||||
Funding support | Japan, 13items
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Citation | Journal: To Be Published Title: Mechanism for drastic reduction in catalytic activity of Trp89Phe-mutated glutamate dehydrogenase revealed by cryoEM-sampling metastable conformation in action Authors: Wakabayashi, T. / Matsui, Y. / Nakasako, M. | ||||||||||||||||||||||||||||||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8zmu.cif.gz | 502.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8zmu.ent.gz | 415.6 KB | Display | PDB format |
PDBx/mmJSON format | 8zmu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8zmu_validation.pdf.gz | 525.8 KB | Display | wwPDB validaton report |
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Full document | 8zmu_full_validation.pdf.gz | 552 KB | Display | |
Data in XML | 8zmu_validation.xml.gz | 93.6 KB | Display | |
Data in CIF | 8zmu_validation.cif.gz | 133.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zm/8zmu ftp://data.pdbj.org/pub/pdb/validation_reports/zm/8zmu | HTTPS FTP |
-Related structure data
Related structure data | 8zneC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 6 molecules ABCDEF
#1: Protein | Mass: 46719.441 Da / Num. of mol.: 6 / Mutation: W89F Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermococcus profundus (archaea) / Gene: gdhA, gdh / Production host: Escherichia coli (E. coli) References: UniProt: O74024, glutamate dehydrogenase [NAD(P)+] |
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-Non-polymers , 5 types, 1010 molecules
#2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-ACY / #4: Chemical | ChemComp-GOL / #5: Chemical | ChemComp-NA / | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | N |
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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: 4.04 Å3/Da / Density % sol: 69.58 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 3.8 Details: 1.6 M lithium sulfate (Wako, Osaka, Japan), 1.7%(w/v) poly-ethylene glycol 8000 (PEG800) (Sigma-Aldrich, St. Louis, USA) and 0.1 M sodium acetate (Wako) |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 1 Å |
Detector | Type: RAYONIX SX-165mm / Detector: CCD / Date: Oct 9, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.028→50 Å / Num. obs: 283125 / % possible obs: 99.8 % / Redundancy: 3.788 % / Rmerge(I) obs: 0.063 / Net I/σ(I): 18.3 |
Reflection shell | Resolution: 2.028→2.07 Å / Rmerge(I) obs: 0.293 / Num. unique obs: 281936 |
-Processing
Software | Name: REFMAC / Version: 5.8.0267 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.028→21.8 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.949 / SU B: 3.285 / SU ML: 0.087 / Cross valid method: THROUGHOUT / ESU R: 0.119 / ESU R Free: 0.115 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 39.29 Å2
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Refinement step | Cycle: 1 / Resolution: 2.028→21.8 Å
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