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Yorodumi- PDB-4lsw: Crystallization and Structural Analysis of 2-Hydroxyacid Dehydrog... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4lsw | ||||||
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Title | Crystallization and Structural Analysis of 2-Hydroxyacid Dehydrogenase from Ketogulonicigenium vulgare Y25 | ||||||
Components | D-2-hydroxyacid dehydrogensase protein | ||||||
Keywords | HYDROLASE / hydrogenase | ||||||
Function / homology | Function and homology information oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / NAD binding Similarity search - Function | ||||||
Biological species | Ketogulonicigenium vulgare (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.64 Å | ||||||
Authors | Han, X. / Liu, X. | ||||||
Citation | Journal: Biotechnol.Lett. / Year: 2014 Title: Crystallization and structural analysis of 2-hydroxyacid dehydrogenase from Ketogulonicigenium vulgare. Authors: Han, X. / Xiong, X. / Hu, X. / Li, M. / Zhang, W. / Liu, X. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4lsw.cif.gz | 82.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4lsw.ent.gz | 61.3 KB | Display | PDB format |
PDBx/mmJSON format | 4lsw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4lsw_validation.pdf.gz | 419.3 KB | Display | wwPDB validaton report |
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Full document | 4lsw_full_validation.pdf.gz | 422.7 KB | Display | |
Data in XML | 4lsw_validation.xml.gz | 17.2 KB | Display | |
Data in CIF | 4lsw_validation.cif.gz | 27.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ls/4lsw ftp://data.pdbj.org/pub/pdb/validation_reports/ls/4lsw | HTTPS FTP |
-Related structure data
Related structure data | 3ba1S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 34394.133 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ketogulonicigenium vulgare (bacteria) / Strain: Y25 / References: UniProt: E3F052 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 6 |
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-Sample preparation
Crystal | Density Matthews: 2.65 Å3/Da / Density % sol: 53.57 % Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN I_PLUS/MINUS COLUMNS |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 23% PEG 3350, 0.2M MgCl, 0.1M pH 7.0 HEPES, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: BSRF / Beamline: 1W2B / Wavelength: 0.9792 Å | ||||||||||||||||||
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Oct 31, 2012 | ||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 | ||||||||||||||||||
Reflection | Resolution: 1.64→50 Å / Num. obs: 38014 / % possible obs: 85 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 | ||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3BA1 Resolution: 1.64→50 Å / SU ML: 0.23 / σ(F): 2 / Phase error: 21.82 / Stereochemistry target values: ML Details: THE ENTRY CONTAINS FRIEDEL PAIRS IN I_PLUS/MINUS COLUMNS
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Solvent computation | Shrinkage radii: 0.47 Å / VDW probe radii: 0.8 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 33.584 Å2 / ksol: 0.435 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.64→50 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14
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