+Open data
-Basic information
Entry | Database: PDB / ID: 1wvg | ||||||
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Title | Structure of CDP-D-glucose 4,6-dehydratase from Salmonella typhi | ||||||
Components | CDP-glucose 4,6-dehydratase | ||||||
Keywords | LYASE / short-chain dehydrogenase/reductase / Rossmann fold | ||||||
Function / homology | Function and homology information CDP-glucose 4,6-dehydratase / CDP-glucose 4,6-dehydratase activity / O antigen biosynthetic process Similarity search - Function | ||||||
Biological species | Salmonella enterica subsp. enterica serovar Typhi (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Koropatkin, N.M. / Holden, H.M. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2005 Title: Structure of CDP-D-glucose 4,6-dehydratase from Salmonella typhi complexed with CDP-D-xylose. Authors: Koropatkin, N.M. / Holden, H.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1wvg.cif.gz | 163.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1wvg.ent.gz | 127.7 KB | Display | PDB format |
PDBx/mmJSON format | 1wvg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1wvg_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 1wvg_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 1wvg_validation.xml.gz | 36.1 KB | Display | |
Data in CIF | 1wvg_validation.cif.gz | 50 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wv/1wvg ftp://data.pdbj.org/pub/pdb/validation_reports/wv/1wvg | HTTPS FTP |
-Related structure data
Similar structure data |
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-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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Details | homotetramer; there is one dimer per asymmetric unit, the tetramer can be generated by 2 fold rotation about the z-axis |
-Components
#1: Protein | Mass: 41030.461 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhi (bacteria) Species: Salmonella enterica / Strain: CT18 / Gene: ddhB / Plasmid: pET-21a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3)pLysS / References: UniProt: P26397, CDP-glucose 4,6-dehydratase #2: Chemical | #3: Chemical | ChemComp-CXY / | #4: 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: 2.4 Å3/Da / Density % sol: 49.3 % |
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Crystal grow | Temperature: 298 K / Method: batch method / pH: 4.2 Details: sodium/potassium phosphate, homopipes, pH 4.2, batch method, temperature 298K |
-Data collection
Diffraction | Mean temperature: 130 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.96411 Å |
Detector | Type: SBC / Detector: CCD / Date: Mar 29, 2004 |
Radiation | Monochromator: double crystal SI-111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.96411 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→50 Å / Num. all: 68364 / Num. obs: 68364 / % possible obs: 94.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.2 % / Rsym value: 0.055 / Net I/σ(I): 37.1 |
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 2.5 % / Mean I/σ(I) obs: 3.1 / Num. unique all: 6117 / Rsym value: 0.248 / % possible all: 85.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: model from MAD experiment performed on Se-Met substituted CDP-D-glucose 4,6-dehydratase from Salmonella typhi Resolution: 1.8→50 Å / σ(F): 0
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Refinement step | Cycle: LAST / Resolution: 1.8→50 Å
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Refine LS restraints |
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