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- PDB-5gg8: Crystal structure of Mycobacterium smegmatis MutT1 in complex wit... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5gg8 | ||||||
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Title | Crystal structure of Mycobacterium smegmatis MutT1 in complex with 8-oxo-dGTP, 8-oxo-dGMP and pyrophosphate (II) | ||||||
![]() | Hydrolase, NUDIX family protein![]() | ||||||
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Function / homology | ![]() 8-oxo-(d)GTP phosphatase / ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Arif, S.M. / Patil, A.G. / Varshney, U. / Vijayan, M. | ||||||
![]() | ![]() Title: Biochemical and structural studies of Mycobacterium smegmatis MutT1, a sanitization enzyme with unusual modes of association Authors: Arif, S.M. / Patil, A.G. / Varshney, U. / Vijayan, M. #1: Journal: Acta Crystallogr.,Sect.F / Year: 2012 Title: Crystallization and preliminary X-ray studies of MutT1 (MSMEG_2390) from Mycobacterium smegmatis Authors: Arif, S.M. / Patil, A.G. / 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 | ![]() | 85.6 KB | Display | ![]() |
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PDB format | ![]() | 59.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5gg5C ![]() 5gg6C ![]() 5gg7C ![]() 5gg9C ![]() 5ggaC ![]() 5ggbC ![]() 5ggcC ![]() 5ggdC ![]() 3fjyS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | ![]() Mass: 38153.148 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: MC2 155 / Gene: MSMEG_2390 / Production host: ![]() ![]() ![]() |
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-Non-polymers , 5 types, 265 molecules ![](data/chem/img/8DG.gif)
![](data/chem/img/8OG.gif)
![](data/chem/img/POP.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/8OG.gif)
![](data/chem/img/POP.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-8DG / |
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#3: Chemical | ChemComp-8OG / |
#4: Chemical | ChemComp-POP / ![]() |
#5: Chemical | ChemComp-MG / |
#6: Water | ChemComp-HOH / ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.03 Å3/Da / Density % sol: 39.41 % |
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Crystal grow![]() | Temperature: 293 K / Method: microbatch / pH: 8.5 Details: 0.2 M sodium acetate trihydrate, 0.1 M TRIS hydrochloride, pH 8.5, 30% w/v PEG 4000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 24, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.85→43.43 Å / Num. obs: 26082 / % possible obs: 100 % / Redundancy: 4.2 % / Net I/σ(I): 9.5 |
Reflection shell | Resolution: 1.85→1.95 Å / Redundancy: 4.2 % / Mean I/σ(I) obs: 2 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 3FJY Resolution: 1.85→43.43 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.955 / SU B: 4.064 / SU ML: 0.117 / Cross valid method: THROUGHOUT / ESU R: 0.144 / ESU R Free: 0.136 / 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: 37.544 Å2
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Refinement step | Cycle: LAST / Resolution: 1.85→43.43 Å
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Refine LS restraints |
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