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Yorodumi- PDB-4wif: Crystal structure of E47Q mutant cytidine deaminase from Mycobact... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4wif | |||||||||
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Title | Crystal structure of E47Q mutant cytidine deaminase from Mycobacterium tuberculosis (MtCDA E47Q) | |||||||||
Components | Cytidine deaminase | |||||||||
Keywords | HYDROLASE / MtCDA E47Q / cytidine deaminase | |||||||||
Function / homology | Function and homology information uridine biosynthetic process / pyrimidine nucleobase salvage / cytidine deaminase / cytidine deamination / deoxycytidine deaminase activity / cytidine deaminase activity / zinc ion binding / metal ion binding / plasma membrane / cytosol Similarity search - Function | |||||||||
Biological species | Mycobacterium tuberculosis (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.8 Å | |||||||||
Authors | Trivella, D.B. / Sanchez-Quitian, A.Z. / Basso, L.A. / Santos, D.S. | |||||||||
Citation | Journal: Rsc Adv / Year: 2015 Title: Crystal structure of E47Q mutant cytidine deaminase from Mycobacterium tuberculosis (MtCDA E47Q) Authors: Sanchez-Quitian, A.Z. / Rodrigues-Junior, V. / Rehm, J.G. / Eichler, P. / Trivella, D.B.B. / Bizarro, C.V. / Basso, L.A. / Santos, D.S. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4wif.cif.gz | 65.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4wif.ent.gz | 47.4 KB | Display | PDB format |
PDBx/mmJSON format | 4wif.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wi/4wif ftp://data.pdbj.org/pub/pdb/validation_reports/wi/4wif | HTTPS FTP |
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-Related structure data
Related structure data | |
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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 on special symmetry positions |
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-Components
#1: Protein | Mass: 14087.157 Da / Num. of mol.: 2 / Mutation: E47Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Production host: Escherichia coli (E. coli) References: UniProt: P9WPH2, UniProt: P9WPH3*PLUS, cytidine deaminase #2: Chemical | #3: 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: 2.53 Å3/Da / Density % sol: 51.38 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1M HEPES pH7.5; 4.3 M Sodium chloride |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.459 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: May 9, 2014 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.459 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.69→111.78 Å / Num. all: 29558 / Num. obs: 29558 / % possible obs: 91.9 % / Redundancy: 2.5 % / Rpim(I) all: 0.046 / Rrim(I) all: 0.079 / Rsym value: 0.064 / Net I/av σ(I): 6.903 / Net I/σ(I): 8.2 / Num. measured all: 72446 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: 0
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-Processing
Software |
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Refinement | Resolution: 1.8→18.65 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.914 / WRfactor Rfree: 0.2575 / WRfactor Rwork: 0.224 / FOM work R set: 0.7962 / SU B: 2.774 / SU ML: 0.089 / SU R Cruickshank DPI: 0.1404 / SU Rfree: 0.1333 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.14 / ESU R Free: 0.133 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 79.19 Å2 / Biso mean: 16.317 Å2 / Biso min: 7.61 Å2
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Refinement step | Cycle: final / Resolution: 1.8→18.65 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.846 Å / Total num. of bins used: 20
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