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- PDB-7dm5: 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: 7dm5 | ||||||
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Title | The structure of the Arabidopsis thaliana guanosine deaminase in reaction with guanosine | ||||||
![]() | Guanosine deaminase | ||||||
![]() | HYDROLASE / deamination / GSDA / purine metabolism / plant protein | ||||||
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: Substrate Specificity of GSDA Revealed by Cocrystal Structures and Binding Studies. Authors: Jia, Q. / Zhang, J. / Zeng, H. / Tang, J. / Xiao, N. / Gao, S. / Li, H. / Xie, W. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 94.9 KB | Display | ![]() |
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PDB format | ![]() | 58 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 7dcbC ![]() 7dcwC ![]() 7dgcC ![]() 7dh1C ![]() 7dm6C ![]() 7dqnC ![]() 7w1qC ![]() 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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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: 2.28 Å3/Da / Density % sol: 46.09 % |
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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: OXFORD ONYX CCD / Detector: CCD / Date: May 12, 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: 2.2→23.56 Å / Num. obs: 16363 / % possible obs: 99.9 % / Redundancy: 6.9 % / Biso Wilson estimate: 15.85 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.11 / Net I/σ(I): 15.1 |
Reflection shell | Resolution: 2.2→2.32 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 5.9 / Num. unique obs: 2364 / CC1/2: 0.944 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 7DBF Resolution: 2.2→23.56 Å / SU ML: 0.1597 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 19.042 / 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: 21.24 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→23.56 Å
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Refine LS restraints |
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LS refinement shell |
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