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Yorodumi- PDB-7dow: The structure of the Arabidopsis thaliana guanosine deaminase in ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7dow | ||||||
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Title | The structure of the Arabidopsis thaliana guanosine deaminase in reaction with 7-deazaguansoine | ||||||
Components | Guanosine deaminase | ||||||
Keywords | PLANT PROTEIN / deamination / GSDA / purine metabolism | ||||||
Function / homology | Function and homology information guanosine deaminase / guanosine deaminase activity / purine nucleoside catabolic process / zinc ion binding / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Arabidopsis thaliana (thale cress) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Xie, W. / Jia, Q. / Zeng, H. | ||||||
Funding support | China, 1items
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Citation | Journal: To Be Published Title: Asymmetric Catalysis of Arabidopsis thaliana Guanosine Deaminase Revealed by Crystal Structures Authors: Xie, W. / Jia, Q. / Zeng, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7dow.cif.gz | 97 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7dow.ent.gz | 58.6 KB | Display | PDB format |
PDBx/mmJSON format | 7dow.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7dow_validation.pdf.gz | 2.2 MB | Display | wwPDB validaton report |
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Full document | 7dow_full_validation.pdf.gz | 2.2 MB | Display | |
Data in XML | 7dow_validation.xml.gz | 17.4 KB | Display | |
Data in CIF | 7dow_validation.cif.gz | 24.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/do/7dow ftp://data.pdbj.org/pub/pdb/validation_reports/do/7dow | HTTPS FTP |
-Related structure data
Related structure data | 7dlcC 7doxC 7doyC 7dpkC 7dbfS S: Starting model for refinement C: citing same article (ref.) |
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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
#1: Protein | Mass: 17523.016 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: GSDA, TAD4, At5g28050 / Production host: Escherichia coli (E. coli) / References: UniProt: Q94BU8, guanosine deaminase #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | 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: 2.32 Å3/Da / Density % sol: 46.93 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 1.2 M Na-citrate and 0.1 M HEPES (pH 7.5) |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å |
Detector | Type: OXFORD ONYX CCD / Detector: CCD / Date: Aug 18, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2→23.66 Å / Num. obs: 21954 / % possible obs: 98.6 % / Redundancy: 7.9 % / Biso Wilson estimate: 16.65 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.073 / Net I/σ(I): 22.5 |
Reflection shell | Resolution: 2→2.11 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 4.4 / Num. unique obs: 3095 / CC1/2: 0.841 / % possible all: 94.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7DBF Resolution: 2→23.66 Å / SU ML: 0.1883 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.9577 / Stereochemistry target values: CDL v1.2
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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: 21.09 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→23.66 Å
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Refine LS restraints |
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LS refinement shell |
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