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Yorodumi- PDB-6k63: The crystal structure of cytidine deaminase from Klebsiella pneumoniae -
+Open data
-Basic information
Entry | Database: PDB / ID: 6k63 | |||||||||
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Title | The crystal structure of cytidine deaminase from Klebsiella pneumoniae | |||||||||
Components | Cytidine deaminase | |||||||||
Keywords | HYDROLASE / Klebsiella pneumoniae / cytidine deaminase / CDA | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Klebsiella pneumoniae subsp. pneumoniae MGH 78578 (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.073 Å | |||||||||
Authors | Liu, W. / Shang, F. / Lan, J. / Chen, Y. / Wang, L. / Xu, Y. | |||||||||
Funding support | China, 2items
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Citation | Journal: Biochem.Biophys.Res.Commun. / Year: 2019 Title: Biochemical and structural analysis of the Klebsiella pneumoniae cytidine deaminase CDA. Authors: Liu, W. / Shang, F. / Chen, Y. / Lan, J. / Wang, L. / Chen, J. / Gao, P. / Ha, N.C. / Quan, C. / Nam, K.H. / Xu, Y. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6k63.cif.gz | 262.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6k63.ent.gz | 208.9 KB | Display | PDB format |
PDBx/mmJSON format | 6k63.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k6/6k63 ftp://data.pdbj.org/pub/pdb/validation_reports/k6/6k63 | HTTPS FTP |
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-Related structure data
Related structure data | 1ctuS 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 31507.664 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Klebsiella pneumoniae subsp. pneumoniae MGH 78578 (bacteria) Strain: MGH 78578 / Gene: cdd / Plasmid: pPROEX-HTA / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A6TBN1, cytidine deaminase #2: Chemical | ChemComp-DIO / #3: Chemical | ChemComp-ZN / #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: 3.17 Å3/Da / Density % sol: 61.18 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 0.1 M HEPES(pH 5.5) 1.72 M Ammonium sulfate 7% v/v 1,4-Dioxane |
-Data collection
Diffraction | Mean temperature: 100 K / Ambient temp details: Liquid nitrogen / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.979617 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 19, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979617 Å / Relative weight: 1 |
Reflection | Resolution: 2.07→50 Å / Num. obs: 96550 / % possible obs: 100 % / Redundancy: 14.1 % / Rsym value: 0.092 / Net I/σ(I): 31 |
Reflection shell | Resolution: 2.07→2.11 Å / Redundancy: 11.6 % / Mean I/σ(I) obs: 7 / Num. unique obs: 9 / Rsym value: 0.295 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1ctu Resolution: 2.073→45.904 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 0.35 / Phase error: 20.73
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.073→45.904 Å
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Refine LS restraints |
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LS refinement shell |
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