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Yorodumi- PDB-3cxr: Crystal structure of gluconate 5-dehydrogase from streptococcus s... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3cxr | ||||||
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Title | Crystal structure of gluconate 5-dehydrogase from streptococcus suis type 2 | ||||||
Components | Dehydrogenase with different specificities | ||||||
Keywords | OXIDOREDUCTASE / Rossmann fold | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Streptococcus suis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Peng, H. / Gao, F. / Zhang, Q. / Liu, Y. / Gao, G.F. | ||||||
Citation | Journal: Protein Sci. / Year: 2009 Title: Structural insight into the catalytic mechanism of gluconate 5-dehydrogenase from Streptococcus suis: Crystal structures of the substrate-free and quaternary complex enzymes. Authors: Zhang, Q. / Peng, H. / Gao, F. / Liu, Y. / Cheng, H. / Thompson, J. / Gao, G.F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3cxr.cif.gz | 64.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3cxr.ent.gz | 46.1 KB | Display | PDB format |
PDBx/mmJSON format | 3cxr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3cxr_validation.pdf.gz | 426.7 KB | Display | wwPDB validaton report |
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Full document | 3cxr_full_validation.pdf.gz | 431.3 KB | Display | |
Data in XML | 3cxr_validation.xml.gz | 12.6 KB | Display | |
Data in CIF | 3cxr_validation.cif.gz | 17.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cx/3cxr ftp://data.pdbj.org/pub/pdb/validation_reports/cx/3cxr | HTTPS FTP |
-Related structure data
Related structure data | 3o03C 1vl8S C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 31056.475 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus suis (bacteria) / Strain: 05HAH33 / Gene: SSU05_1225, IdnO / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: A4VVQ2, gluconate 5-dehydrogenase |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.11 Å3/Da / Density % sol: 41.66 % |
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-Data collection
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å |
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Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→59.66 Å / Num. obs: 19757 |
Reflection shell | Resolution: 1.9→30.56 Å / Mean I/σ(I) obs: 4.2 / Num. unique all: 19757 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1vl8 Resolution: 2→30.56 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.944 / SU B: 2.905 / SU ML: 0.085 / Cross valid method: THROUGHOUT / ESU R: 0.194 / ESU R Free: 0.15 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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 mean: 22.88 Å2
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Refinement step | Cycle: LAST / Resolution: 2→30.56 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.052 Å / Total num. of bins used: 20
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