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- PDB-7x9o: Crystal structure of MutT-8-oxo-dGMP complex with Mg2+ ions: Reac... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7x9o | ||||||
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Title | Crystal structure of MutT-8-oxo-dGMP complex with Mg2+ ions: Reaction using Mg2+ | ||||||
![]() | 7,8-dihydro-8-oxoguanine-triphosphatase | ||||||
![]() | HYDROLASE / Nudix hydrolase | ||||||
Function / homology | ![]() 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 | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Nakamura, T. / Yamagata, Y. | ||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 52.4 KB | Display | ![]() |
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PDB format | ![]() | 30.3 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 | ![]() | 9.4 KB | Display | |
Data in CIF | ![]() | 12.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7ww5C ![]() 7ww6C ![]() 7ww7C ![]() 7ww8C ![]() 7ww9C ![]() 7wwaC ![]() 7x9hC ![]() 7x9iC ![]() 7x9jC ![]() 7x9kC ![]() 7x9lC ![]() 7x9nC ![]() 3a6tS S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components
-Protein / Sugars , 2 types, 2 molecules A
#1: Protein | Mass: 14945.029 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: A0A037YRW7, 8-oxo-dGTP diphosphatase, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides |
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#2: Polysaccharide | beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose |
-Non-polymers , 4 types, 155 molecules ![](data/chem/img/8OG.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-8OG / | ||
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#4: Chemical | ChemComp-SO4 / | ||
#5: Chemical | #6: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.13 Å3/Da / Density % sol: 42.26 % |
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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: ![]() ![]() ![]() |
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: 1.58→40.66 Å / Num. obs: 17461 / % possible obs: 96.2 % / Redundancy: 4.7 % / Biso Wilson estimate: 11.23 Å2 / Rmerge(I) obs: 0.087 / Net I/σ(I): 13.1 |
Reflection shell | Resolution: 1.58→1.61 Å / Rmerge(I) obs: 0.443 / Num. unique obs: 792 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3A6T Resolution: 1.58→40.66 Å / SU ML: 0.1163 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 18.0319 / 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: 15.21 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.58→40.66 Å
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Refine LS restraints |
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LS refinement shell |
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