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Yorodumi- PDB-7x9n: Crystal structure of MutT-8-oxo-dGTP complex with three Mg2+ ions... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7x9n | ||||||
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Title | Crystal structure of MutT-8-oxo-dGTP complex with three Mg2+ ions: Reaction using Mg2+ | ||||||
Components | 7,8-dihydro-8-oxoguanine-triphosphatase | ||||||
Keywords | HYDROLASE / Nudix hydrolase | ||||||
Function / homology | Function and homology information 8-oxo-dGTP diphosphatase / 8-oxo-GDP phosphatase activity / 8-oxo-dGDP phosphatase activity / 8-oxo-7,8-dihydrodeoxyguanosine triphosphate pyrophosphatase activity / 8-oxo-7,8-dihydroguanosine triphosphate pyrophosphatase activity / DNA replication / DNA repair / metal ion binding Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.7 Å | ||||||
Authors | Nakamura, T. / Yamagata, Y. | ||||||
Funding support | Japan, 1items
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Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2022 Title: Visualization of mutagenic nucleotide processing by Escherichia coli MutT, a Nudix hydrolase. Authors: Nakamura, T. / Yamagata, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7x9n.cif.gz | 52.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7x9n.ent.gz | 31.2 KB | Display | PDB format |
PDBx/mmJSON format | 7x9n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7x9n_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 7x9n_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 7x9n_validation.xml.gz | 9.6 KB | Display | |
Data in CIF | 7x9n_validation.cif.gz | 12.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x9/7x9n ftp://data.pdbj.org/pub/pdb/validation_reports/x9/7x9n | HTTPS FTP |
-Related structure data
Related structure data | 7ww5C 7ww6C 7ww7C 7ww8C 7ww9C 7wwaC 7x9hC 7x9iC 7x9jC 7x9kC 7x9lC 7x9oC 3a6tS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 14945.029 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) References: UniProt: A0A037YRW7, 8-oxo-dGTP diphosphatase, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides |
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-Non-polymers , 5 types, 143 molecules
#2: Chemical | ChemComp-SO4 / | ||
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#3: Chemical | ChemComp-8DG / | ||
#4: Chemical | ChemComp-8OG / | ||
#5: Chemical | #6: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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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: 2.12 Å3/Da / Density % sol: 41.97 % |
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Crystal grow | Temperature: 288 K / Method: vapor diffusion, hanging drop Details: potassium sodium tartrate, sodium citrate, ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1.1 Å |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Feb 14, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→31.63 Å / Num. obs: 14231 / % possible obs: 98.2 % / Redundancy: 4.3 % / Biso Wilson estimate: 13.22 Å2 / Rsym value: 0.123 / Net I/σ(I): 17.1 |
Reflection shell | Resolution: 1.7→1.73 Å / Rmerge(I) obs: 0.301 / Num. unique obs: 610 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 3A6T Resolution: 1.7→31.63 Å / SU ML: 0.1732 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 18.924 / Stereochemistry target values: GeoStd + Monomer Library
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.44 Å2 | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→31.63 Å
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Refine LS restraints |
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LS refinement shell |
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