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- PDB-5gg6: 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: 5gg6 | ||||||
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Title | Crystal structure of Mycobacterium smegmatis MutT1 in complex with 8-oxo-dGTP | ||||||
![]() | Hydrolase, NUDIX family protein | ||||||
![]() | HYDROLASE / 8-oxo-guanine nucleotides / sanitization of nucleotide pool / nudix enzyme / histidine phosphatase domain / binding sites at intermolecular interface / enzyme action | ||||||
Function / homology | ![]() 8-oxo-(d)GTP phosphatase / diadenosine hexaphosphate hydrolase (ATP-forming) / 8-oxo-dGDP phosphatase / 8-oxo-GDP phosphatase activity / 8-oxo-dGDP phosphatase activity / 8-oxo-7,8-dihydroguanosine triphosphate pyrophosphatase activity / DNA replication / DNA repair / metal ion binding 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 | ![]() | 149.4 KB | Display | ![]() |
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PDB format | ![]() | 112.9 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 | ![]() | 30.1 KB | Display | |
Data in CIF | ![]() | 45 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5gg5C ![]() 5gg7C ![]() 5gg8C ![]() 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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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 38153.148 Da / Num. of mol.: 2 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, 555 molecules ![](data/chem/img/8DG.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-CL / #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.98 Å3/Da / Density % sol: 37.94 % |
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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, 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: Feb 19, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.95372 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→49.36 Å / Num. obs: 59643 / % possible obs: 99.4 % / Redundancy: 5 % / Net I/σ(I): 9.8 |
Reflection shell | Resolution: 1.75→1.84 Å / Redundancy: 5 % / Mean I/σ(I) obs: 1.9 / % possible all: 98.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3FJY Resolution: 1.75→49.36 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.959 / SU B: 3.092 / SU ML: 0.095 / Cross valid method: THROUGHOUT / ESU R: 0.112 / ESU R Free: 0.111 / 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: 31.378 Å2
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Refinement step | Cycle: LAST / Resolution: 1.75→49.36 Å
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Refine LS restraints |
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