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Yorodumi- PDB-1uxi: Large improvement in the thermal stability of a tetrameric malate... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1uxi | |||||||||
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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 (NAD+) activity / lactate metabolic process / L-lactate dehydrogenase activity / pyruvate metabolic process / tricarboxylic acid cycle / cytoplasm Similarity search - Function | |||||||||
Biological species | CHLOROFLEXUS AURANTIACUS (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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 | 1uxi.cif.gz | 138.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1uxi.ent.gz | 107.9 KB | Display | PDB format |
PDBx/mmJSON format | 1uxi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1uxi_validation.pdf.gz | 1003.3 KB | Display | wwPDB validaton report |
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Full document | 1uxi_full_validation.pdf.gz | 1020.9 KB | Display | |
Data in XML | 1uxi_validation.xml.gz | 31.5 KB | Display | |
Data in CIF | 1uxi_validation.cif.gz | 44.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ux/1uxi ftp://data.pdbj.org/pub/pdb/validation_reports/ux/1uxi | HTTPS FTP |
-Related structure data
Related structure data | 1uxgC 1uxhC 1uxjC 1uxkC 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
#1: Protein | Mass: 32747.811 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 #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-NA / | #5: Water | ChemComp-HOH / | 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: 4.85 Å3/Da / Density % sol: 74 % |
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Crystal grow | pH: 6.5 / Details: 20-40% PEG400, 100 MM NASUCCINATE, PH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X31 / Wavelength: 1 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→25 Å / Num. obs: 74855 / % possible obs: 91.4 % / Redundancy: 5.4 % / Rmerge(I) obs: 0.089 / Net I/σ(I): 20.5 |
Reflection shell | Resolution: 2.1→2.18 Å / Rmerge(I) obs: 0.53 / Mean I/σ(I) obs: 3.7 / % possible all: 83.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1GUY Resolution: 2.1→25 Å / Cross valid method: THROUGHOUT / σ(F): 2
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 66.7 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.7 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.1→25 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.18 Å / Total num. of bins used: 10
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