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Yorodumi- PDB-5xd4: Crystal structure of Mycobacterium smegmatis MutT1 in complex wit... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5xd4 | ||||||
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Title | Crystal structure of Mycobacterium smegmatis MutT1 in complex with ATP (II) | ||||||
Components | NUDIX family proteinNudix hydrolase | ||||||
Keywords | HYDROLASE / Nudix enzyme / histidine phosphatase domain / intermolecular interface binding / diadenosine polyphosphates / enzyme action / fluoride inhibition | ||||||
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 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.47 Å | ||||||
Authors | Arif, S.M. / Varshney, U. / Vijayan, M. | ||||||
Citation | Journal: J. Struct. Biol. / Year: 2017 Title: Hydrolysis of diadenosine polyphosphates. Exploration of an additional role of Mycobacterium smegmatis MutT1 Authors: Arif, S.M. / Varshney, U. / Vijayan, M. #1: Journal: Acta Crystallogr. D Biol. Crystallogr. / 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. #2: Journal: Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun. 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 | 5xd4.cif.gz | 156.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5xd4.ent.gz | 119.6 KB | Display | PDB format |
PDBx/mmJSON format | 5xd4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xd/5xd4 ftp://data.pdbj.org/pub/pdb/validation_reports/xd/5xd4 | HTTPS FTP |
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-Related structure data
Related structure data | 5xd1C 5xd2C 5xd3C 5xd5C 5gg5S 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 (strain ATCC 700084 / mc(2)155) (bacteria) Strain: ATCC 700084 / mc(2)155 / Gene: MSMEG_2390 / Production host: Escherichia coli (E. coli) / Strain (production host): JW0097 / References: UniProt: A0QUZ2 | ||||||
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#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-MG / | #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: 2.01 Å3/Da / Density % sol: 38.68 % |
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Crystal grow | Temperature: 293 K / Method: microbatch / pH: 8.5 Details: 0.2M sodium acetate trihydrate, 0.1M Tris-HCl pH 8.5, 30%(w/v) PEG4000 |
-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 20, 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: 1.47→43.34 Å / Num. obs: 50952 / % possible obs: 99.6 % / Redundancy: 4.2 % / Net I/σ(I): 10 |
Reflection shell | Resolution: 1.47→1.55 Å / Redundancy: 3.9 % / Mean I/σ(I) obs: 1.6 / Num. unique obs: 7339 / % possible all: 98 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5gg5 Resolution: 1.47→43.34 Å / Cor.coef. Fo:Fc: 0.984 / Cor.coef. Fo:Fc free: 0.975 / SU B: 2.79 / SU ML: 0.044 / Cross valid method: THROUGHOUT / ESU R: 0.064 / ESU R Free: 0.058 / 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: 28.454 Å2
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Refinement step | Cycle: 1 / Resolution: 1.47→43.34 Å
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Refine LS restraints |
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