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Yorodumi- PDB-5gud: Glutamate dehydrogenase from Corynebacterium glutamicum (alpha-im... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5gud | ||||||
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Title | Glutamate dehydrogenase from Corynebacterium glutamicum (alpha-iminoglutarate/NADP+ complex) | ||||||
Components | Glutamate dehydrogenase | ||||||
Keywords | OXIDOREDUCTASE / ROSSMANN FOLD / GLUTAMATE DEHYDROGENASE | ||||||
Function / homology | Function and homology information oxidoreductase activity, acting on the CH-NH2 group of donors, NAD or NADP as acceptor / amino acid metabolic process / nucleotide binding Similarity search - Function | ||||||
Biological species | Corynebacterium glutamicum (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.68 Å | ||||||
Authors | Tomita, T. / Nishiyama, M. | ||||||
Funding support | Japan, 1items
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Citation | Journal: FEBS Lett. / Year: 2017 Title: Crystal structure of the 2-iminoglutarate-bound complex of glutamate dehydrogenase from Corynebacterium glutamicum Authors: Tomita, T. / Yin, L. / Nakamura, S. / Kosono, S. / Kuzuyama, T. / Nishiyama, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5gud.cif.gz | 588.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5gud.ent.gz | 477.2 KB | Display | PDB format |
PDBx/mmJSON format | 5gud.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5gud_validation.pdf.gz | 2.4 MB | Display | wwPDB validaton report |
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Full document | 5gud_full_validation.pdf.gz | 2.5 MB | Display | |
Data in XML | 5gud_validation.xml.gz | 125.5 KB | Display | |
Data in CIF | 5gud_validation.cif.gz | 185.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gu/5gud ftp://data.pdbj.org/pub/pdb/validation_reports/gu/5gud | HTTPS FTP |
-Related structure data
Related structure data | 3aogS S: Starting model for refinement |
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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
-Protein , 1 types, 6 molecules ABCDEF
#1: Protein | Mass: 51766.113 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Corynebacterium glutamicum (bacteria) / Gene: APT58_10030 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0U4QBJ6 |
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-Non-polymers , 5 types, 2793 molecules
#2: Chemical | ChemComp-2IT / ( #3: Chemical | ChemComp-NDP / #4: Chemical | ChemComp-K / #5: Chemical | ChemComp-CIT / | #6: 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: 2.31 Å3/Da / Density % sol: 46.71 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 100MM HEPES-NAOH (PH8.0), 21% PEG 3350, 200MM POTASSIUM CITRATE |
-Data collection
Diffraction | Mean temperature: 95 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: May 25, 2012 / Details: MIRRORS |
Radiation | Monochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.68→50 Å / Num. obs: 319184 / % possible obs: 97 % / Observed criterion σ(I): 2.4 / Redundancy: 3.7 % / Rmerge(I) obs: 0.069 / Net I/σ(I): 22.7 |
Reflection shell | Resolution: 1.68→1.71 Å / Rmerge(I) obs: 0.334 / % possible all: 94.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3AOG Resolution: 1.68→30.83 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.932 / SU B: 2.021 / SU ML: 0.069 / Cross valid method: THROUGHOUT / σ(F): 2.4 / ESU R: 0.115 / ESU R Free: 0.111 / 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: 1.4 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.48 Å2
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Refinement step | Cycle: LAST / Resolution: 1.68→30.83 Å
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Refine LS restraints |
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