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Yorodumi- PDB-4p9c: Crystal structure of dCMP deaminase from the cyanophage S-TIM5 in... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4p9c | ||||||
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Title | Crystal structure of dCMP deaminase from the cyanophage S-TIM5 in complex with dCMP and dUMP | ||||||
Components | Deoxycytidylate deaminase | ||||||
Keywords | HYDROLASE / dCMP deaminase / cytidine deaminase / deoxycytidylate deaminase / S-TIM5 | ||||||
Function / homology | Function and homology information dCMP deaminase activity / pyrimidine nucleotide metabolic process / nucleotide binding / zinc ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Cyanophage S-TIM5 (virus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.6 Å | ||||||
Authors | Marx, A. / Alian, A. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2015 Title: The First Crystal Structure of a dTTP-bound Deoxycytidylate Deaminase Validates and Details the Allosteric-Inhibitor Binding Site. Authors: Marx, A. / Alian, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4p9c.cif.gz | 335.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4p9c.ent.gz | 273.9 KB | Display | PDB format |
PDBx/mmJSON format | 4p9c.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4p9c_validation.pdf.gz | 7.3 MB | Display | wwPDB validaton report |
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Full document | 4p9c_full_validation.pdf.gz | 7.3 MB | Display | |
Data in XML | 4p9c_validation.xml.gz | 75.7 KB | Display | |
Data in CIF | 4p9c_validation.cif.gz | 90.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p9/4p9c ftp://data.pdbj.org/pub/pdb/validation_reports/p9/4p9c | HTTPS FTP |
-Related 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: 15191.383 Da / Num. of mol.: 12 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Cyanophage S-TIM5 (virus) / Production host: Escherichia coli (E. coli) / References: UniProt: H6WFU3 #2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-DCM / #4: Chemical | ChemComp-DU / #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.73 Å3/Da / Density % sol: 54.88 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.1M MMT buffer pH 8, 25% (w/v) PEG 1500, 5mM Magnesium chloride and 5mM dCTP |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9322 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 15, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9322 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→99.99 Å |
Reflection shell | Resolution: 2.6→2.67 Å / % possible all: 100 |
-Processing
Software |
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Refinement | Resolution: 2.6→99.99 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.911 / SU B: 0.002 / SU ML: 0 / Cross valid method: THROUGHOUT / ESU R: 0.297 / ESU R Free: 0.344 / 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: 36.493 Å2
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Refinement step | Cycle: 1 / Resolution: 2.6→99.99 Å
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LS refinement shell | Resolution: 2.6→2.667 Å / Total num. of bins used: 20
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