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Open data
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Basic information
Entry | Database: PDB / ID: 5zrl | ||||||
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Title | M. smegmatis antimutator protein MutT2 in complex with CDP | ||||||
![]() | Putative mutator protein MutT2/NUDIX hydrolase | ||||||
![]() | HYDROLASE / Nudix hydrolase / MutT / antimutator / CTP pyrophosphorylase / CTP | ||||||
Function / homology | ![]() 8-oxo-dGTP diphosphatase / 8-oxo-GDP phosphatase activity / 8-oxo-dGDP phosphatase activity / 8-oxo-7,8-dihydrodeoxyguanosine triphosphate pyrophosphatase activity / 8-oxo-7,8-dihydroguanosine triphosphate pyrophosphatase activity / DNA replication / DNA repair / nucleotide binding / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Singh, A. / Arif, S.M. / Sang, P.B. / Varshney, U. / Vijayan, M. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 74.3 KB | Display | ![]() |
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PDB format | ![]() | 52.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 15.8 KB | Display | |
Data in CIF | ![]() | 23.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5zrcSC ![]() 5zrgC ![]() 5zrhC ![]() 5zriC ![]() 5zrkC ![]() 5zroC ![]() 5zrpC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: LYS / Beg label comp-ID: LYS / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: _ / Auth seq-ID: 3 - 127 / Label seq-ID: 23 - 147
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Components
#1: Protein | Mass: 16081.142 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: ATCC 700084 / mc(2)155 / Gene: mutT2, MSMEI_5016 / Production host: ![]() ![]() #2: Chemical | #3: Chemical | ChemComp-EDO / | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.11 Å3/Da / Density % sol: 40.21 % |
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Crystal grow | Temperature: 292 K / Method: microbatch Details: 0.2 M Ammonium acetate, 0.1 M Sodium citrate tribasic dihydrate pH 5.6, 30% w/v PEG 4000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Sep 8, 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: 1.6→30.76 Å / Num. obs: 33778 / % possible obs: 98.7 % / Redundancy: 7.1 % / Rmerge(I) obs: 0.127 / Net I/σ(I): 9.1 |
Reflection shell | Resolution: 1.6→1.69 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.721 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 4542 / % possible all: 91.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5ZRC Resolution: 1.61→30.76 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.922 / SU B: 2.222 / SU ML: 0.077 / Cross valid method: THROUGHOUT / ESU R: 0.105 / ESU R Free: 0.104 / 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: 17.474 Å2
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Refinement step | Cycle: 1 / Resolution: 1.61→30.76 Å
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Refine LS restraints |
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