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Yorodumi- PDB-7ecr: Crystal Structure of Aspergillus terreus Glutamate Dehydrogenase ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7ecr | ||||||
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Title | Crystal Structure of Aspergillus terreus Glutamate Dehydrogenase (AtGDH) Complexed With Succinate and ADP-ribose | ||||||
Components | Glutamate dehydrogenase | ||||||
Keywords | OXIDOREDUCTASE / Glutamate dehydrogenase / allostery / Aspergillus / enzyme mechanism | ||||||
Function / homology | Function and homology information glutamate biosynthetic process / glutamate dehydrogenase (NADP+) activity / nucleotide binding / cytosol Similarity search - Function | ||||||
Biological species | Aspergillus terreus (mold) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.73 Å | ||||||
Authors | Godsora, B.K.J. / Prakash, P. / Punekar, N.S. / Bhaumik, P. | ||||||
Funding support | India, 1items
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Citation | Journal: Proteins / Year: 2022 Title: Molecular insights into the inhibition of glutamate dehydrogenase by the dicarboxylic acid metabolites. Authors: Godsora, B.K.J. / Prakash, P. / Punekar, N.S. / Bhaumik, P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7ecr.cif.gz | 313.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7ecr.ent.gz | 248.4 KB | Display | PDB format |
PDBx/mmJSON format | 7ecr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ec/7ecr ftp://data.pdbj.org/pub/pdb/validation_reports/ec/7ecr | HTTPS FTP |
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-Related structure data
Related structure data | 7ecsC 7ectC 5xvxS S: Starting model for refinement C: citing same article (ref.) |
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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 on special symmetry positions |
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-Components
#1: Protein | Mass: 49247.438 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Details: Succinate and ADP-ribose / Source: (gene. exp.) Aspergillus terreus (mold) / Gene: gdhA, ATETN484_0007063400 / Production host: Escherichia coli (E. coli) / References: UniProt: T2D1F5 #2: Chemical | ChemComp-GOL / #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 4.06 Å3/Da / Density % sol: 69.68 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.8 M Succinic acid, pH 7.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jul 6, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.73→38.68 Å / Num. obs: 246054 / % possible obs: 99.2 % / Redundancy: 7.11 % / CC1/2: 0.99 / Rmerge(I) obs: 0.11 / Rrim(I) all: 0.11 / Net I/σ(I): 15.38 |
Reflection shell | Resolution: 1.73→1.83 Å / Redundancy: 5.93 % / Rmerge(I) obs: 0.91 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 36141 / CC1/2: 0.72 / Rrim(I) all: 0.1 / % possible all: 94.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5XVX Resolution: 1.73→38.68 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.966 / SU B: 1.649 / SU ML: 0.05 / Cross valid method: THROUGHOUT / ESU R: 0.066 / ESU R Free: 0.068 / 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: 19.827 Å2
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Refinement step | Cycle: 1 / Resolution: 1.73→38.68 Å
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Refine LS restraints |
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