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Yorodumi- PDB-8rwl: Crystal structure of Methanopyrus kandleri malate dehydrogenase m... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8rwl | |||||||||
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Title | Crystal structure of Methanopyrus kandleri malate dehydrogenase mutant 1 | |||||||||
Components | Malate dehydrogenase | |||||||||
Keywords | OXIDOREDUCTASE / malate dehydrogenase / Rossmann-like motif / NAD(P)H binding site | |||||||||
Function / homology | Function and homology information malate dehydrogenase [NAD(P)+] / L-malate dehydrogenase (NADP+) activity / L-malate dehydrogenase (NAD+) activity / lactate metabolic process / L-lactate dehydrogenase activity / pyruvate metabolic process / tricarboxylic acid cycle Similarity search - Function | |||||||||
Biological species | Methanopyrus kandleri (archaea) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | |||||||||
Authors | Coquille, S. / Roche, J. / Engilberge, S. / Girard, E. / Madern, D. | |||||||||
Funding support | France, 2items
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Citation | Journal: To Be Published Title: Navigating the conformational landscape of an enzyme. Stabilization of a low populated conformer by evolutionary mutations triggers Allostery into a non-allosteric enzyme. Authors: Coquille, S. / Simoes Pereira, C. / Brochier-Armanet, C. / Roche, J. / Santoni, G. / Coquelle, N. / Girard, E. / Sterpone, F. / Madern, D. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8rwl.cif.gz | 388.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8rwl.ent.gz | 290.7 KB | Display | PDB format |
PDBx/mmJSON format | 8rwl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8rwl_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 8rwl_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 8rwl_validation.xml.gz | 24.7 KB | Display | |
Data in CIF | 8rwl_validation.cif.gz | 34.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rw/8rwl ftp://data.pdbj.org/pub/pdb/validation_reports/rw/8rwl | HTTPS FTP |
-Related structure data
Related structure data | 8rs5C 9endC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 34625.836 Da / Num. of mol.: 2 / Mutation: R85Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methanopyrus kandleri (archaea) / Gene: mdh, MK1069 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8TWG5, malate dehydrogenase [NAD(P)+] |
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-Non-polymers , 5 types, 153 molecules
#2: Chemical | #3: Chemical | ChemComp-GOL / #4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Details
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: 2.78 Å3/Da / Density % sol: 55.71 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 10 mM Hepes pH 7.5, 30% PEG 300 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.966 Å |
Detector | Type: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Sep 7, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.966 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→20 Å / Num. obs: 35833 / % possible obs: 99.9 % / Redundancy: 18.25 % / Biso Wilson estimate: 55.33 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.062 / Rrim(I) all: 0.064 / Net I/σ(I): 27.84 |
Reflection shell | Resolution: 2.3→2.36 Å / Rmerge(I) obs: 1.032 / Mean I/σ(I) obs: 1.67 / Num. unique obs: 2568 / CC1/2: 0.578 / Rrim(I) all: 1.113 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→19.92 Å / SU ML: 0.2617 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 25.0945 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 74 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→19.92 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group | Refine-ID: X-RAY DIFFRACTION
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