- PDB-5xko: Crystal structure of native Msmeg3575 deaminase from Mycobacteriu... -
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ID or keywords:
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Basic information
Entry
Database: PDB / ID: 5xko
Title
Crystal structure of native Msmeg3575 deaminase from Mycobacterium smegmatis
Components
Cytidine/deoxycytidylate deaminase, zinc-binding region
Keywords
HYDROLASE / deaminase / CDA fold / mutagens
Function / homology
Function and homology information
cytidine metabolic process / pyrimidine-containing compound salvage / cytosine deaminase activity / cytosine metabolic process / metal ion binding / cytoplasm Similarity search - Function
Cytidine and deoxycytidylate deaminase zinc-binding region / Cytidine and deoxycytidylate deaminase domain / Cytidine and deoxycytidylate deaminases domain profile. / Cytidine deaminase-like Similarity search - Domain/homology
ACETATE ION / CACODYLATE ION / Cytidine/deoxycytidylate deaminase, zinc-binding region Similarity search - Component
Biological species
Mycobacterium smegmatis (bacteria)
Method
X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.89 Å
Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 1, 2016
Radiation
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 1.28 Å / Relative weight: 1
Reflection
Resolution: 1.89→47.8 Å / Num. obs: 29961 / % possible obs: 99.8 % / Redundancy: 39.8 % / Rsym value: 0.073 / Net I/σ(I): 73
Reflection shell
Resolution: 1.89→2 Å / % possible all: 99.3
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Processing
Software
Name
Version
Classification
REFMAC
5.8.0135
refinement
HKL-3000
datareduction
HKL-3000
datascaling
SHELXCD
phasing
Refinement
Method to determine structure: SAD / Resolution: 1.89→47.8 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.949 / SU B: 2.083 / SU ML: 0.063 / Cross valid method: THROUGHOUT / ESU R: 0.108 / ESU R Free: 0.108 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.178
1988
6.7 %
RANDOM
Rwork
0.138
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obs
0.141
27732
99.3 %
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Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å