[English] 日本語
Yorodumi- PDB-5xw0: Crystal Structure of Aspergillus niger Glutamate Dehydrogenase Co... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5xw0 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure of Aspergillus niger Glutamate Dehydrogenase Complexed With Isophthalate and NADPH | ||||||
Components | Glutamate dehydrogenase | ||||||
Keywords | OXIDOREDUCTASE / Aspergillus / Glutamate / Dehydrogenase / Isophthalate / Inhibition / NADPH / Coenzyme / Reaction mechanism | ||||||
Function / homology | Function and homology information glutamate dehydrogenase (NADP+) activity / amino acid metabolic process / nucleotide binding Similarity search - Function | ||||||
Biological species | Aspergillus niger (mold) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Prakash, P. / Punekar, N.S. / Bhaumik, P. | ||||||
Funding support | India, 1items
| ||||||
Citation | Journal: J. Biol. Chem. / Year: 2018 Title: Structural basis for the catalytic mechanism and alpha-ketoglutarate cooperativity of glutamate dehydrogenase. Authors: Prakash, P. / Punekar, N.S. / Bhaumik, P. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5xw0.cif.gz | 113.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5xw0.ent.gz | 87 KB | Display | PDB format |
PDBx/mmJSON format | 5xw0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xw/5xw0 ftp://data.pdbj.org/pub/pdb/validation_reports/xw/5xw0 | HTTPS FTP |
---|
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| x 6||||||||||||
Unit cell |
| ||||||||||||
Components on special symmetry positions |
|
-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 49442.508 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aspergillus niger (mold) Production host: Escherichia coli-Thermus thermophilus shuttle vector pTRH1T (others) References: UniProt: B6V7E4 |
---|
-Non-polymers , 5 types, 326 molecules
#2: Chemical | ChemComp-NDP / | ||||
---|---|---|---|---|---|
#3: Chemical | ChemComp-8G0 / | ||||
#4: Chemical | ChemComp-GOL / #5: Chemical | ChemComp-PEG / #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 7.06 Å3/Da / Density % sol: 82.58 % |
---|---|
Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6 Details: 0.1 M MES (pH 6.0) 30% (v/v) PEG 200, 5 % (w/v) PEG 3000 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.9763 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 3, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→70 Å / Num. obs: 109208 / % possible obs: 99.9 % / Redundancy: 7.4 % / CC1/2: 0.99 / Rmerge(I) obs: 0.054 / Net I/σ(I): 24.3 |
Reflection shell | Resolution: 1.9→2 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 4.5 / Num. unique obs: 15446 / CC1/2: 0.61 / % possible all: 98.8 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→40 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.961 / SU B: 1.719 / SU ML: 0.049 / Cross valid method: THROUGHOUT / ESU R: 0.069 / ESU R Free: 0.068 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 31.006 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 1.9→40 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|