+Open data
-Basic information
Entry | Database: PDB / ID: 5gg5 | ||||||
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Title | Crystal structure of Mycobacterium smegmatis MutT1 | ||||||
Components | Hydrolase, NUDIX family protein | ||||||
Keywords | HYDROLASE / 8-oxo-guanine nucleotides / sanitization of nucleotide pool / nudix enzyme / histidine phosphatase domain / binding sites at intermolecular interface / enzyme action | ||||||
Function / homology | Function and homology information 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 | Mycobacterium smegmatis str. MC2 155 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.64 Å | ||||||
Authors | Arif, S.M. / Patil, A.G. / Varshney, U. / Vijayan, M. | ||||||
Citation | Journal: Acta Crystallogr D Struct Biol / Year: 2017 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5gg5.cif.gz | 90.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5gg5.ent.gz | 65.8 KB | Display | PDB format |
PDBx/mmJSON format | 5gg5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gg/5gg5 ftp://data.pdbj.org/pub/pdb/validation_reports/gg/5gg5 | HTTPS FTP |
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-Related structure data
Related structure data | 5gg6C 5gg7C 5gg8C 5gg9C 5ggaC 5ggbC 5ggcC 5ggdC 3fjyS C: citing same article (ref.) S: Starting model for refinement |
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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
#1: Protein | Mass: 38153.148 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium smegmatis str. MC2 155 (bacteria) Strain: MC2 155 / Gene: MSMEG_2390 / Production host: Escherichia coli (E. coli) / Strain (production host): JW0097 / References: UniProt: A0QUZ2 | ||||||
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#2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-EDO / #4: Chemical | #5: 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: 2.18 Å3/Da / Density % sol: 43.54 % |
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Crystal grow | Temperature: 293 K / Method: microbatch / pH: 6.5 Details: 0.2 M ammonium sulfate, 0.1 M MES monohydrate, 30% w/v PEG monomethyl ether 5000, 0.01M TCEP hydrochloride |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.95372 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 25, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.95372 Å / Relative weight: 1 |
Reflection | Resolution: 1.64→43.85 Å / Num. obs: 41476 / % possible obs: 99.4 % / Redundancy: 3.6 % / Net I/σ(I): 11.4 |
Reflection shell | Resolution: 1.64→1.73 Å / Redundancy: 3.2 % / Mean I/σ(I) obs: 3.6 / % possible all: 96.3 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3FJY Resolution: 1.64→43.85 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.942 / SU B: 1.657 / SU ML: 0.056 / Cross valid method: THROUGHOUT / ESU R: 0.085 / ESU R Free: 0.09 / 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: 17.092 Å2
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Refinement step | Cycle: LAST / Resolution: 1.64→43.85 Å
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Refine LS restraints |
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