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Yorodumi- PDB-5ujk: Malate dehydrogenase from Methylobacterium extorquens, complexed ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5ujk | ||||||
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Title | Malate dehydrogenase from Methylobacterium extorquens, complexed with NAD | ||||||
Components | Malate dehydrogenase | ||||||
Keywords | OXIDOREDUCTASE / malate / dehydrogenase / NAD | ||||||
Function / homology | Function and homology information malate dehydrogenase / L-malate dehydrogenase activity / carboxylic acid metabolic process / tricarboxylic acid cycle Similarity search - Function | ||||||
Biological species | Methylobacterium extorquens (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.53 Å | ||||||
Authors | Gonzalez, J.M. | ||||||
Citation | Journal: Acta Crystallogr F Struct Biol Commun / Year: 2018 Title: Conformational changes on substrate binding revealed by structures of Methylobacterium extorquens malate dehydrogenase. Authors: Gonzalez, J.M. / Marti-Arbona, R. / Chen, J.C.H. / Broom-Peltz, B. / Unkefer, C.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ujk.cif.gz | 138.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ujk.ent.gz | 106.5 KB | Display | PDB format |
PDBx/mmJSON format | 5ujk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uj/5ujk ftp://data.pdbj.org/pub/pdb/validation_reports/uj/5ujk | HTTPS FTP |
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-Related structure data
Related structure data | 5ulvC 4ropS 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: 33681.648 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methylobacterium extorquens (bacteria) / Gene: mdh / Production host: Escherichia coli (E. coli) References: UniProt: A9W386, UniProt: Q84FY8*PLUS, malate dehydrogenase | ||||
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#2: Chemical | ChemComp-NAD / | ||||
#3: Chemical | #4: Chemical | ChemComp-CL / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.62 Å3/Da / Density % sol: 52.99 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 25-28% PEG400, 180-220mM CaCl2, 0.1M Hepes pH 7.5, soaked with 1mM NAD |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å |
Detector | Type: RAYONIX MX-300 / Detector: CCD / Date: Feb 10, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97949 Å / Relative weight: 1 |
Reflection | Resolution: 1.53→54.09 Å / Num. obs: 54696 / % possible obs: 100 % / Redundancy: 10.6 % / CC1/2: 0.998 / Rmerge(I) obs: 0.108 / Rpim(I) all: 0.033 / Net I/σ(I): 12.1 |
Reflection shell | Resolution: 1.53→1.56 Å / Redundancy: 9 % / Rmerge(I) obs: 0.8 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 2651 / CC1/2: 0.733 / Rpim(I) all: 0.357 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4rop Resolution: 1.53→54.09 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.961 / SU B: 2.392 / SU ML: 0.041 / Cross valid method: THROUGHOUT / ESU R: 0.058 / ESU R Free: 0.063 / 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: 24.517 Å2
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Refinement step | Cycle: 1 / Resolution: 1.53→54.09 Å
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