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Yorodumi- PDB-3kb6: Crystal structure of D-Lactate dehydrogenase from aquifex aeolicu... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3kb6 | ||||||||||||
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Title | Crystal structure of D-Lactate dehydrogenase from aquifex aeolicus complexed with NAD and Lactic acid | ||||||||||||
Components | D-lactate dehydrogenase | ||||||||||||
Keywords | OXIDOREDUCTASE / D-LDH / NAD / STRUCTURAL GENOMICS / NPPSFA / NATIONAL PROJECT ON PROTEIN STRUCTURAL AND FUNCTIONAL ANALYSES / RIKEN STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE / RSGI | ||||||||||||
Function / homology | Function and homology information | ||||||||||||
Biological species | Aquifex aeolicus (bacteria) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.12 Å | ||||||||||||
Authors | Antonyuk, S.V. / Strange, R.W. / Ellis, M.J. / Bessho, Y. / Kuramitsu, S. / Yokoyama, S. / Hasnain, S.S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||||||||
Citation | Journal: Acta Crystallogr.,Sect.F / Year: 2009 Title: Structure of D-lactate dehydrogenase from Aquifex aeolicus complexed with NAD(+) and lactic acid (or pyruvate). Authors: Antonyuk, S.V. / Strange, R.W. / Ellis, M.J. / Bessho, Y. / Kuramitsu, S. / Inoue, Y. / Yokoyama, S. / Hasnain, S.S. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3kb6.cif.gz | 307 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3kb6.ent.gz | 251 KB | Display | PDB format |
PDBx/mmJSON format | 3kb6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3kb6_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 3kb6_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 3kb6_validation.xml.gz | 62.2 KB | Display | |
Data in CIF | 3kb6_validation.cif.gz | 88 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kb/3kb6 ftp://data.pdbj.org/pub/pdb/validation_reports/kb/3kb6 | HTTPS FTP |
-Related structure data
Related structure data | 2dldS S: Starting model for refinement |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 38458.578 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aquifex aeolicus (bacteria) / Strain: VF5 / Gene: aq_727, ldhA / Plasmid: pET-21a / Production host: Escherichia coli (E. coli) / Strain (production host): ROSETTA834(DE3) / References: UniProt: O66939, D-lactate dehydrogenase |
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-Non-polymers , 7 types, 895 molecules
#2: Chemical | ChemComp-PPI / #3: Chemical | ChemComp-LAC / #4: Chemical | ChemComp-NAD / #5: Chemical | ChemComp-PEG / #6: Chemical | ChemComp-1PE / #7: Chemical | ChemComp-GOL / #8: 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: 2.64 Å3/Da / Density % sol: 53.33 % / Mosaicity: 0.386 ° |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6 Details: 25% PEG 200, 0.1M MES pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX10.1 / Wavelength: 0.98 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 1, 2007 / Details: MIRRORS |
Radiation | Monochromator: SAGITALLY FOCUSED SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.12→38 Å / Num. obs: 88902 / % possible obs: 95.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8 % / Biso Wilson estimate: 24.4 Å2 / Rmerge(I) obs: 0.088 / Χ2: 1.206 / Net I/σ(I): 12.2 |
Reflection shell | Resolution: 2.12→2.2 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.306 / Mean I/σ(I) obs: 5.3 / Num. unique all: 7005 / Χ2: 1.207 / % possible all: 76.3 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2DLD Resolution: 2.12→38 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.937 / Occupancy max: 1 / Occupancy min: 0 / SU B: 4.323 / SU ML: 0.114 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.21 / ESU R Free: 0.177 / 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: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 76.88 Å2 / Biso mean: 29.453 Å2 / Biso min: 9.15 Å2
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Refinement step | Cycle: LAST / Resolution: 2.12→38 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.12→2.175 Å / Total num. of bins used: 20
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