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Open data
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Basic information
Entry | Database: PDB / ID: 6oha | |||||||||
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Title | Yeast Guanine Deaminase | |||||||||
![]() | Probable guanine deaminase | |||||||||
![]() | HYDROLASE / amidohydrolase guanine deaminase purine metabolism | |||||||||
Function / homology | ![]() Purine catabolism / guanine deaminase / guanine deaminase activity / guanine catabolic process / deaminase activity / guanine metabolic process / zinc ion binding / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Shek, R.S. / French, J.B. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural Determinants for Substrate Selectivity in Guanine Deaminase Enzymes of the Amidohydrolase Superfamily. Authors: Shek, R. / Hilaire, T. / Sim, J. / French, J.B. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 227 KB | Display | ![]() |
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PDB format | ![]() | 146.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 288.7 KB | Display | ![]() |
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Full document | ![]() | 289.4 KB | Display | |
Data in XML | ![]() | 2 KB | Display | |
Data in CIF | ![]() | 8.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6oh9C ![]() 6ohbC ![]() 6ohcC ![]() 2oodS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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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 on special symmetry positions |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 55269.410 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: ATCC 204508 / S288c / Gene: GUD1, YDL238C / Production host: ![]() ![]() |
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-Non-polymers , 5 types, 283 molecules ![](data/chem/img/XAN.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/1PE.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/1PE.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-XAN / | ||||
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#3: Chemical | ChemComp-ZN / | ||||
#4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.21 Å3/Da / Density % sol: 61.72 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop Details: 17% Peg 3350 0.2 M ammonium sulfate 100 mM Hepes, pH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Aug 15, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9201 Å / Relative weight: 1 |
Reflection | Resolution: 2.21→29.07 Å / Num. obs: 33428 / % possible obs: 99.1 % / Redundancy: 8.8 % / Biso Wilson estimate: 32.73 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.146 / Net I/σ(I): 10 |
Reflection shell | Resolution: 2.21→2.29 Å / Rmerge(I) obs: 0.973 / Num. unique obs: 3075 / CC1/2: 0.696 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2OOD Resolution: 2.21→29.07 Å / SU ML: 0.2169 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.2395
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 34.42 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.21→29.07 Å
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Refine LS restraints |
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LS refinement shell |
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