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- PDB-7doy: The structure of the Arabidopsis thaliana guanosine deaminase in ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7doy | ||||||
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Title | The structure of the Arabidopsis thaliana guanosine deaminase in complex with 6-O-methylguanosine | ||||||
![]() | Guanosine deaminase | ||||||
![]() | PLANT PROTEIN / deamination / GSDA / purine metabolism | ||||||
Function / homology | ![]() guanosine deaminase / guanosine deaminase activity / purine nucleoside catabolic process / zinc ion binding / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Xie, W. / Jia, Q. / Zeng, H. | ||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 92.6 KB | Display | ![]() |
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PDB format | ![]() | 56.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 7dlcC ![]() 7dowC ![]() 7doxC ![]() 7dpkC ![]() 7dbfS S: Starting model for refinement C: citing same article ( |
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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
#1: Protein | Mass: 17523.016 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.32 Å3/Da / Density % sol: 47.04 % |
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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: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Apr 17, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.17→50 Å / Num. obs: 17386 / % possible obs: 100 % / Redundancy: 19.8 % / Biso Wilson estimate: 29.92 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.177 / Rrim(I) all: 0.18 / Net I/σ(I): 25.6 |
Reflection shell | Resolution: 2.17→2.25 Å / Redundancy: 17.7 % / Rmerge(I) obs: 0.501 / Mean I/σ(I) obs: 6.333 / Num. unique obs: 1711 / CC1/2: 0.952 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 7DBF Resolution: 2.17→28.61 Å / SU ML: 0.1931 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 21.8036 / 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: 35.7 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.17→28.61 Å
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Refine LS restraints |
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LS refinement shell |
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