+Open data
-Basic information
Entry | Database: PDB / ID: 6oha | |||||||||
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Title | Yeast Guanine Deaminase | |||||||||
Components | Probable guanine deaminase | |||||||||
Keywords | HYDROLASE / amidohydrolase guanine deaminase purine metabolism | |||||||||
Function / homology | Function and homology information Purine catabolism / guanine deaminase / guanine deaminase activity / guanine catabolic process / deaminase activity / guanine metabolic process / zinc ion binding / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.21 Å | |||||||||
Authors | Shek, R.S. / French, J.B. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Biochemistry / Year: 2019 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6oha.cif.gz | 227 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6oha.ent.gz | 146.4 KB | Display | PDB format |
PDBx/mmJSON format | 6oha.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oh/6oha ftp://data.pdbj.org/pub/pdb/validation_reports/oh/6oha | HTTPS FTP |
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-Related structure data
Related structure data | 6oh9C 6ohbC 6ohcC 2oodS 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 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.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / Gene: GUD1, YDL238C / Production host: Escherichia coli (E. coli) / References: UniProt: Q07729, guanine deaminase |
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-Non-polymers , 5 types, 283 molecules
#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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.9201 Å |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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