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Yorodumi- PDB-7bya: Malate Dehydrogenase from Geobacillus stearothermophilus (gs-MDH)... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7bya | |||||||||
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Title | Malate Dehydrogenase from Geobacillus stearothermophilus (gs-MDH) complexed with Oxaloacetic Acid (OAA) and Adenosine 5'-Diphosphoribose (APR) | |||||||||
Components | Malate dehydrogenase | |||||||||
Keywords | OXIDOREDUCTASE / Malate Dehydrogenase | |||||||||
Function / homology | Function and homology information malate dehydrogenase / L-malate dehydrogenase activity / carboxylic acid metabolic process / tricarboxylic acid cycle Similarity search - Function | |||||||||
Biological species | Geobacillus stearothermophilus (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | |||||||||
Authors | Shimozawa, Y. / Nakamura, T. / Himiyama, T. / Nishiya, Y. | |||||||||
Funding support | Japan, 2items
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Citation | Journal: J.Biochem. / Year: 2021 Title: Structural analysis and reaction mechanism of malate dehydrogenase from Geobacillus stearothermophilus. Authors: Shimozawa, Y. / Himiyama, T. / Nakamura, T. / Nishiya, Y. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7bya.cif.gz | 258.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7bya.ent.gz | 199.4 KB | Display | PDB format |
PDBx/mmJSON format | 7bya.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/by/7bya ftp://data.pdbj.org/pub/pdb/validation_reports/by/7bya | HTTPS FTP |
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-Related structure data
Related structure data | 7by8SC 7by9C 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
#1: Protein | Mass: 35932.312 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Geobacillus stearothermophilus (bacteria) Gene: mdh / Production host: Escherichia coli (E. coli) / References: UniProt: A0A143T1U9, malate dehydrogenase #2: Chemical | ChemComp-APR / #3: Chemical | ChemComp-OAA / | #4: 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: 2.4 Å3/Da / Density % sol: 48.77 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.1 M Tris-HCl (pH 7.0), 16 % PEG 2000 MME, 2 mM OAA, and 2 mM NAD+ |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å |
Detector | Type: DECTRIS EIGER X 4M / Detector: PIXEL / Date: May 21, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→49.16 Å / Num. obs: 66776 / % possible obs: 100 % / Redundancy: 27.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.111 / Net I/σ(I): 21.8 |
Reflection shell | Resolution: 2.2→2.25 Å / Rmerge(I) obs: 0.441 / Mean I/σ(I) obs: 8.1 / Num. unique obs: 4459 / CC1/2: 0.99 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7BY8 Resolution: 2.2→49.159 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.934 / WRfactor Rfree: 0.239 / WRfactor Rwork: 0.185 / SU B: 5.733 / SU ML: 0.148 / Average fsc free: 0.9153 / Average fsc work: 0.9326 / Cross valid method: THROUGHOUT / ESU R: 0.257 / ESU R Free: 0.202 Details: Hydrogens have been added in their 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: BABINET MODEL PLUS MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 48.842 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→49.159 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20 / % reflection obs: 100 %
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