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Yorodumi- PDB-1uxk: Large improvement in the thermal stability of a tetrameric malate... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1uxk | ||||||
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Title | Large improvement in the thermal stability of a tetrameric malate dehydrogenase by single point mutations at the dimer-dimer interface | ||||||
Components | MALATE DEHYDROGENASE | ||||||
Keywords | OXIDOREDUCTASE / TRICARBOXYLIC ACID CYCLE / MALATE DEHYDROGENASE | ||||||
Function / homology | Function and homology information malate dehydrogenase / L-malate dehydrogenase activity / carboxylic acid metabolic process / tricarboxylic acid cycle / cytoplasm Similarity search - Function | ||||||
Biological species | CHLOROFLEXUS AURANTIACUS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Bjork, A. / Dalhus, B. / Mantzilas, D. / Eijsink, V.G.H. / Sirevag, R. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2004 Title: Large Improvement in the Thermal Stability of a Tetrameric Malate Dehydrogenase by Single Point Mutations at the Dimer-Dimer Interface. Authors: Bjork, A. / Dalhus, B. / Mantzilas, D. / Sirevag, R. / Eijsink, V.G.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1uxk.cif.gz | 143.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1uxk.ent.gz | 110.5 KB | Display | PDB format |
PDBx/mmJSON format | 1uxk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ux/1uxk ftp://data.pdbj.org/pub/pdb/validation_reports/ux/1uxk | HTTPS FTP |
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-Related structure data
Related structure data | 1uxgC 1uxhC 1uxiC 1uxjC 1guyS 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
-Protein , 1 types, 2 molecules AC
#1: Protein | Mass: 32746.760 Da / Num. of mol.: 2 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) CHLOROFLEXUS AURANTIACUS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P80040, malate dehydrogenase |
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-Non-polymers , 5 types, 662 molecules
#2: Chemical | #3: Chemical | ChemComp-CD / #4: Chemical | #5: Chemical | ChemComp-NA / #6: Water | ChemComp-HOH / | |
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-Details
Compound details | ENGINEERED |
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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: 2.5 Å3/Da / Density % sol: 48 % |
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Crystal grow | pH: 4.5 / Details: 10-20% PEG400, NA ACETATE PH 4.5, 40MM CDCL2 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X31 / Wavelength: 1.1 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→25 Å / Num. obs: 55441 / % possible obs: 90.7 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.043 / Net I/σ(I): 19.5 |
Reflection shell | Resolution: 1.8→1.86 Å / Rmerge(I) obs: 0.53 / Mean I/σ(I) obs: 2.1 / % possible all: 68 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1GUY Resolution: 1.8→25 Å / Cross valid method: THROUGHOUT / σ(F): 2
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 52.7 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.8 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.8→25 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.86 Å / Total num. of bins used: 10
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