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Yorodumi- PDB-6itk: Crystal structure of malate dehydrogenase from Corynebacterium gl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6itk | ||||||
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Title | Crystal structure of malate dehydrogenase from Corynebacterium glutamicum ATCC 13032 in complex with NAD and malate | ||||||
Components | Malate dehydrogenase | ||||||
Keywords | OXIDOREDUCTASE / dehydrogenase | ||||||
Function / homology | Function and homology information malate dehydrogenase / L-malate dehydrogenase (NAD+) activity / malate metabolic process / tricarboxylic acid cycle / carbohydrate metabolic process Similarity search - Function | ||||||
Biological species | Corynebacterium glutamicum ATCC 13032 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Seo, H. / Kim, K.-J. | ||||||
Citation | Journal: Nat Commun / Year: 2020 Title: Enhanced succinic acid production by Mannheimia employing optimal malate dehydrogenase. Authors: Ahn, J.H. / Seo, H. / Park, W. / Seok, J. / Lee, J.A. / Kim, W.J. / Kim, G.B. / Kim, K.J. / Lee, S.Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6itk.cif.gz | 138.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6itk.ent.gz | 106.7 KB | Display | PDB format |
PDBx/mmJSON format | 6itk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/it/6itk ftp://data.pdbj.org/pub/pdb/validation_reports/it/6itk | HTTPS FTP |
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-Related structure data
Related structure data | 6itlC 4tvoS 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: 36011.082 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Corynebacterium glutamicum ATCC 13032 (bacteria) Strain: ATCC 13032 / DSM 20300 / JCM 1318 / LMG 3730 / NCIMB 10025 Gene: mdh, Cgl2380, cg2613 / Plasmid: pET30a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q8NN33, malate dehydrogenase #2: Chemical | #3: Chemical | #4: 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: 2.75 Å3/Da / Density % sol: 55.21 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: PEG 3350, HEPES, MgCl2 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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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: Dec 18, 2016 |
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→77.08 Å / Num. obs: 50050 / % possible obs: 96.3 % / Redundancy: 2.7 % / Rmerge(I) obs: 0.123 / Net I/σ(I): 18 |
Reflection shell | Resolution: 2→2.03 Å / Rmerge(I) obs: 0.39 / Num. unique obs: 2392 / CC1/2: 0.792 / % possible all: 93 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4TVO Resolution: 2→26.73 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.925 / SU B: 4.883 / SU ML: 0.128 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.17 / ESU R Free: 0.155 / Stereochemistry target values: MAXIMUM LIKELIHOOD 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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 89.39 Å2 / Biso mean: 24.369 Å2 / Biso min: 12.24 Å2
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Refinement step | Cycle: final / Resolution: 2→26.73 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.003→2.055 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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