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Yorodumi- PDB-6ihd: Crystal structure of Malate dehydrogenase from Metallosphaera sedula -
+Open data
-Basic information
Entry | Database: PDB / ID: 6ihd | ||||||
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Title | Crystal structure of Malate dehydrogenase from Metallosphaera sedula | ||||||
Components | Malate dehydrogenase | ||||||
Keywords | OXIDOREDUCTASE | ||||||
Function / homology | Function and homology information carboxylic acid metabolic process / oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor Similarity search - Function | ||||||
Biological species | Metallosphaera sedula (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Lee, D. / Kim, K.J. | ||||||
Citation | Journal: Biochem. Biophys. Res. Commun. / Year: 2019 Title: Crystal structure and biochemical characterization of malate dehydrogenase from Metallosphaera sedula Authors: Lee, D. / Hong, J. / Kim, K.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ihd.cif.gz | 130.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ihd.ent.gz | 101.2 KB | Display | PDB format |
PDBx/mmJSON format | 6ihd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6ihd_validation.pdf.gz | 996.7 KB | Display | wwPDB validaton report |
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Full document | 6ihd_full_validation.pdf.gz | 1002 KB | Display | |
Data in XML | 6ihd_validation.xml.gz | 24.1 KB | Display | |
Data in CIF | 6ihd_validation.cif.gz | 33 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ih/6ihd ftp://data.pdbj.org/pub/pdb/validation_reports/ih/6ihd | HTTPS FTP |
-Related structure data
Related structure data | 6iheC 4plhS 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: 33349.500 Da / Num. of mol.: 2 / Fragment: UNP residues 2-306 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Metallosphaera sedula (archaea) / Strain: DSM 5348 / Gene: HA72_0455 / Plasmid: pET30a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21_T1R(DE3) / References: UniProt: A0A088E2H7, malate dehydrogenase #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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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: 3.36 Å3/Da / Density % sol: 63.34 % / Mosaicity: 0.861 ° |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 35 %(v/v) 2-ethoxyethanol, 0.1M sodium cacodylate / hydrochloric acid pH 6.0 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97934 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Feb 28, 2017 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Double Crystal Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97934 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.3→50 Å / Num. obs: 40297 / % possible obs: 97.7 % / Redundancy: 11.3 % / Rmerge(I) obs: 0.075 / Rpim(I) all: 0.02 / Rrim(I) all: 0.078 / Χ2: 2.716 / Net I/σ(I): 15.3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4PLH Resolution: 2.3→50 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.936 / SU B: 6.772 / SU ML: 0.156 / σ(F): 0 / ESU R: 0.218 / ESU R Free: 0.202 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 137.64 Å2 / Biso mean: 53.705 Å2
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Refinement step | Cycle: final / Resolution: 2.3→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.301→2.361 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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