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Yorodumi- PDB-7f8d: Malate Dehydrogenase from Geobacillus stearothermophilus (gs-MDH)... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7f8d | ||||||||||||
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Title | Malate Dehydrogenase from Geobacillus stearothermophilus (gs-MDH) G218Y mutant | ||||||||||||
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: 2.4 Å | ||||||||||||
Authors | Shimozawa, Y. / Himiyama, T. / Nakamura, T. / Nishiya, Y. | ||||||||||||
Funding support | Japan, 3items
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Citation | Journal: Protein Eng.Des.Sel. / Year: 2021 Title: Increasing loop flexibility affords low-temperature adaptation of a moderate thermophilic 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 | 7f8d.cif.gz | 258.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7f8d.ent.gz | 202.3 KB | Display | PDB format |
PDBx/mmJSON format | 7f8d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f8/7f8d ftp://data.pdbj.org/pub/pdb/validation_reports/f8/7f8d | HTTPS FTP |
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-Related structure data
Related structure data | 7by8S 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
#1: Protein | Mass: 36038.434 Da / Num. of mol.: 4 / Mutation: G218Y 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-NAD / #3: Water | ChemComp-HOH / | 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: 2.23 Å3/Da / Density % sol: 44.9 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 20 mM Tris-HCl (pH 7.0), 12% PEG 8000, 0.2 M magnesium chloride, 2 mM oxaloacetic acid, 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: 2.4→48.51 Å / Num. obs: 51272 / % possible obs: 100 % / Redundancy: 13.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.091 / Net I/σ(I): 21.6 |
Reflection shell | Resolution: 2.4→2.47 Å / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 7.7 / Num. unique obs: 4381 / CC1/2: 0.973 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7BY8 Resolution: 2.4→48.509 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.891 / SU B: 8.224 / SU ML: 0.196 / Cross valid method: THROUGHOUT / ESU R: 0.46 / ESU R Free: 0.284 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: 1.4 Å / Solvent model: BABINET MODEL PLUS MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 50.407 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4→48.509 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
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