+Open data
-Basic information
Entry | Database: PDB / ID: 5zrh | ||||||
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Title | M. smegmatis antimutator protein MutT2 in complex with CMP | ||||||
Components | Putative mutator protein MutT2/NUDIX hydrolase | ||||||
Keywords | HYDROLASE / Nudix hydrolase / MutT / antimutator / CTP pyrophosphorylase / CMP | ||||||
Function / homology | Function and homology information 8-oxo-dGTP diphosphatase / DNA replication / hydrolase activity / DNA repair / metal ion binding Similarity search - Function | ||||||
Biological species | Mycobacterium smegmatis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.54 Å | ||||||
Authors | Singh, A. / Arif, S.M. / Sang, P.B. / Varshney, U. / Vijayan, M. | ||||||
Citation | Journal: J.Struct.Biol. / Year: 2018 Title: Structural insights into the specificity and catalytic mechanism of mycobacterial nucleotide pool sanitizing enzyme MutT2. Authors: Singh, A. / Mohammad Arif, S. / Biak Sang, P. / Varshney, U. / Vijayan, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5zrh.cif.gz | 46.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5zrh.ent.gz | 30.3 KB | Display | PDB format |
PDBx/mmJSON format | 5zrh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zr/5zrh ftp://data.pdbj.org/pub/pdb/validation_reports/zr/5zrh | HTTPS FTP |
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-Related structure data
Related structure data | 5zrcSC 5zrgC 5zriC 5zrkC 5zrlC 5zroC 5zrpC S: Starting model for refinement C: citing same article (ref.) |
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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: 16081.142 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria) Strain: ATCC 700084 / mc(2)155 / Gene: mutT2, MSMEI_5016 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: I7FJF7, UniProt: A0R2K6*PLUS |
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#2: Chemical | ChemComp-EDO / |
#3: Chemical | ChemComp-C5P / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.95 Å3/Da / Density % sol: 35.31 % |
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Crystal grow | Temperature: 292 K / Method: microbatch Details: 0.1 M Imidazole pH 6.5, 1.0 M Sodium acetate trihydrate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.54179 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Sep 14, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54179 Å / Relative weight: 1 |
Reflection | Resolution: 1.54→28.74 Å / Num. obs: 18346 / % possible obs: 98.3 % / Redundancy: 13.1 % / Rmerge(I) obs: 0.075 / Net I/σ(I): 24.6 |
Reflection shell | Resolution: 1.54→1.63 Å / Redundancy: 12.1 % / Rmerge(I) obs: 0.586 / Mean I/σ(I) obs: 4.6 / Num. unique obs: 2429 / % possible all: 91.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5ZRC Resolution: 1.54→28.74 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.944 / SU B: 1.408 / SU ML: 0.052 / Cross valid method: THROUGHOUT / ESU R: 0.082 / ESU R Free: 0.086 / 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: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.926 Å2
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Refinement step | Cycle: 1 / Resolution: 1.54→28.74 Å
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Refine LS restraints |
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