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- PDB-6m72: 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: 6m72 | ||||||
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Title | Crystal structure of Mycobacterium smegmatis MutT1 in complex with 8-oxo-dGDP | ||||||
![]() | Hydrolase, NUDIX family protein | ||||||
![]() | HYDROLASE / MsMutT1 / Nudix hydrolase / histidine phosphatase domain / Nucleotide pool sanitation enzyme / 8-oxo-dGDP / Molecular aggregation / plasticity / 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 | ![]() ![]() ![]() ![]() | ||||||
![]() | Raj, P. / Karthik, S. / Arif, S.M. / Varshney, U. / Vijayan, M. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Plasticity, ligand conformation and enzyme action of Mycobacterium smegmatis MutT1. Authors: Raj, P. / Karthik, S. / Arif, S.M. / Varshney, U. / Vijayan, M. #1: ![]() 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. #2: ![]() Title: Hydrolysis of diadenosine polyphosphates. Exploration of an additional role of Mycobacterium smegmatis MutT1. Authors: Arif, S.M. / 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 | ![]() | 88.7 KB | Display | ![]() |
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PDB format | ![]() | 61.8 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 | ![]() | 17.5 KB | Display | |
Data in CIF | ![]() | 27 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6m65C ![]() 6m69C ![]() 6m6yC ![]() 5gg5S C: citing same article ( S: Starting model for refinement |
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Similar structure data | |
Experimental dataset #1 | Data reference: ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#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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#2: Chemical | ChemComp-8GD / |
#3: Chemical | ChemComp-POP / |
#4: Chemical | ChemComp-MG / |
#5: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.1 Å3/Da / Density % sol: 41.25 % |
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Crystal grow | Temperature: 298 K / Method: microbatch / pH: 4.6 Details: 0.2 M ammonium acetate, 0.1 M sodium acetate trihydrate, 30% w/v PEG 4000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 21, 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: 1.6→40.49 Å / Num. obs: 42971 / % possible obs: 99.4 % / Redundancy: 4.9 % / CC1/2: 0.983 / Rpim(I) all: 0.073 / Rrim(I) all: 0.167 / Rsym value: 0.149 / Net I/av σ(I): 2.5 / Net I/σ(I): 5.7 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5GG5 Resolution: 1.6→36.65 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.932 / SU B: 2.436 / SU ML: 0.083 / SU R Cruickshank DPI: 0.1009 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.101 / ESU R Free: 0.105 / Details: Individual isotropic B-factor refinement
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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 max: 81.72 Å2 / Biso mean: 20.223 Å2 / Biso min: 9.77 Å2
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Refinement step | Cycle: final / Resolution: 1.6→36.65 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.641 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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