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Yorodumi- PDB-5ggc: Crystal structure of Mycobacterium smegmatis MutT1 in complex wit... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5ggc | ||||||
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Title | Crystal structure of Mycobacterium smegmatis MutT1 in complex with phosphate and magnesium ions (excess magnesium, I) | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 1.85 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 | 5ggc.cif.gz | 142.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ggc.ent.gz | 107.8 KB | Display | PDB format |
PDBx/mmJSON format | 5ggc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gg/5ggc ftp://data.pdbj.org/pub/pdb/validation_reports/gg/5ggc | HTTPS FTP |
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-Related structure data
Related structure data | 5gg5C 5gg6C 5gg7C 5gg8C 5gg9C 5ggaC 5ggbC 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 38153.148 Da / Num. of mol.: 2 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 #2: Chemical | #3: Chemical | ChemComp-MG / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2 Å3/Da / Density % sol: 38.52 % |
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Crystal grow | Temperature: 293 K / Method: microbatch / pH: 8.5 Details: 0.2 M magnesium chloride hexahydrate, 0.1 M TRIS hydrochloride, 30% w/v PEG 4000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.54179 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Aug 1, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54179 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→31.97 Å / Num. obs: 51169 / % possible obs: 99.8 % / Redundancy: 5.3 % / Net I/σ(I): 7.6 |
Reflection shell | Resolution: 1.85→1.95 Å / Redundancy: 5.2 % / Mean I/σ(I) obs: 1.9 / % possible all: 99.3 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3FJY Resolution: 1.85→31.97 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.936 / SU B: 6.463 / SU ML: 0.172 / Cross valid method: THROUGHOUT / ESU R: 0.178 / ESU R Free: 0.163 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.627 Å2
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Refinement step | Cycle: LAST / Resolution: 1.85→31.97 Å
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Refine LS restraints |
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