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Yorodumi- PDB-4p9d: Crystal structure of dCMP deaminase from the cyanophage S-TIM5 in... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4p9d | ||||||
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Title | Crystal structure of dCMP deaminase from the cyanophage S-TIM5 in complex with dTMP and dTTP. | ||||||
Components | Deoxycytidylate deaminase | ||||||
Keywords | HYDROLASE / deoxycytidylate deaminase / dCMP deaminase / cytidine deaminase / S-TIM5 cyanophage | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 2.9 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 | 4p9d.cif.gz | 175.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4p9d.ent.gz | 139.5 KB | Display | PDB format |
PDBx/mmJSON format | 4p9d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4p9d_validation.pdf.gz | 3.7 MB | Display | wwPDB validaton report |
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Full document | 4p9d_full_validation.pdf.gz | 3.8 MB | Display | |
Data in XML | 4p9d_validation.xml.gz | 37.9 KB | Display | |
Data in CIF | 4p9d_validation.cif.gz | 45.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p9/4p9d ftp://data.pdbj.org/pub/pdb/validation_reports/p9/4p9d | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 6 molecules ABCDEF
#1: Protein | Mass: 15191.383 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Cyanophage S-TIM5 (virus) / Production host: Escherichia coli (E. coli) / References: UniProt: H6WFU3 |
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-Non-polymers , 6 types, 64 molecules
#2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-MG / #4: Chemical | ChemComp-TTP / #5: Chemical | ChemComp-TMP / #6: Chemical | #7: 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: 2.08 Å3/Da / Density % sol: 40.9 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.2M Potassium formate, 20% (w/v) PEG 3350, 5mM Magnesium chloride and 5mM dTTP |
-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: 2.9→67.02 Å / Num. obs: 17452 / % possible obs: 99.8 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.089 / Net I/σ(I): 11.7 |
Reflection shell | Resolution: 2.9→3.06 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.349 / Mean I/σ(I) obs: 4 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→67.022 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 25.71 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.9→67.022 Å
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Refine LS restraints |
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LS refinement shell |
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