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Yorodumi- PDB-1wvc: alpha-D-glucose-1-phosphate cytidylyltransferase complexed with CTP -
+Open data
-Basic information
Entry | Database: PDB / ID: 1wvc | ||||||
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Title | alpha-D-glucose-1-phosphate cytidylyltransferase complexed with CTP | ||||||
Components | Glucose-1-phosphate cytidylyltransferase | ||||||
Keywords | TRANSFERASE / CDP-glucose pyrophosphorylase / nucleotidyltransferase | ||||||
Function / homology | Function and homology information glucose-1-phosphate cytidylyltransferase / glucose-1-phosphate cytidylyltransferase activity / O antigen biosynthetic process / nucleotide binding / metal ion binding Similarity search - Function | ||||||
Biological species | Salmonella enterica subsp. enterica serovar Typhi (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Koropatkin, N.M. / Cleland, W.W. / Holden, H.M. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2005 Title: Kinetic and structural analysis of alpha-D-Glucose-1-phosphate cytidylyltransferase from Salmonella typhi. Authors: Koropatkin, N.M. / Cleland, W.W. / 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 | 1wvc.cif.gz | 68.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1wvc.ent.gz | 49 KB | Display | PDB format |
PDBx/mmJSON format | 1wvc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1wvc_validation.pdf.gz | 765.2 KB | Display | wwPDB validaton report |
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Full document | 1wvc_full_validation.pdf.gz | 783.8 KB | Display | |
Data in XML | 1wvc_validation.xml.gz | 10.5 KB | Display | |
Data in CIF | 1wvc_validation.cif.gz | 14.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wv/1wvc ftp://data.pdbj.org/pub/pdb/validation_reports/wv/1wvc | HTTPS FTP |
-Related structure data
Related structure data | 1tzfS 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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Unit cell |
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-Components
#1: Protein | Mass: 29203.598 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhi (bacteria) Species: Salmonella enterica / Strain: CT18 / Gene: rfbF / Plasmid: pET-28a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3)pLysS References: UniProt: P26396, UniProt: Q8Z5I4*PLUS, glucose-1-phosphate cytidylyltransferase | ||||||
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#2: Chemical | #3: Chemical | ChemComp-NI / | #4: Chemical | ChemComp-CTP / | #5: 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: 3 Å3/Da / Density % sol: 58.3 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 Details: PEG 400, magnesium chloride, HEPES, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K |
-Data collection
Diffraction | Mean temperature: 130 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 32-ID / Wavelength: 0.9641 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Aug 6, 2004 |
Radiation | Monochromator: Diamond 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9641 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→25 Å / Num. all: 11780 / Num. obs: 11780 / % possible obs: 97.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.5 % / Rsym value: 0.062 / Net I/σ(I): 26.4 |
Reflection shell | Resolution: 2.5→2.59 Å / Redundancy: 5.3 % / Mean I/σ(I) obs: 3.1 / Num. unique all: 1064 / Rsym value: 0.274 / % possible all: 90.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1TZF Resolution: 2.5→25 Å / σ(F): 0.5
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Refinement step | Cycle: LAST / Resolution: 2.5→25 Å
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Refine LS restraints |
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