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- PDB-4xj5: Crystal structure of Vibrio cholerae DncV 3'-deoxy GTP bound form -
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Open data
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Basic information
Entry | Database: PDB / ID: 4xj5 | ||||||
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Title | Crystal structure of Vibrio cholerae DncV 3'-deoxy GTP bound form | ||||||
![]() | Cyclic AMP-GMP synthase | ||||||
![]() | TRANSFERASE / Cyclic GMP-AMP synthase / Bacterial virulence / nucleotidyltransferase | ||||||
Function / homology | ![]() 3',3'-cyclic GMP-AMP synthase activity / cyclic nucleotide biosynthetic process / negative regulation of chemotaxis / diguanylate cyclase activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / defense response to virus / GTP binding / ATP binding / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kato, K. / Ishii, R. / Ishitani, R. / Nureki, O. | ||||||
![]() | ![]() Title: Structural Basis for the Catalytic Mechanism of DncV, Bacterial Homolog of Cyclic GMP-AMP Synthase Authors: Kato, K. / Ishii, R. / Hirano, S. / Ishitani, R. / Nureki, O. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 172.4 KB | Display | ![]() |
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PDB format | ![]() | 134.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 18.4 KB | Display | |
Data in CIF | ![]() | 27 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4xj1SC ![]() 4xj3C ![]() 4xj4C ![]() 4xj6C 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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 44313.566 Da / Num. of mol.: 1 / Fragment: UNP residues 1-215,242-412 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: N16961 / Gene: dncV, VC_0179 / Production host: ![]() ![]() References: UniProt: Q9KVG7, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases |
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-Non-polymers , 5 types, 255 molecules ![](data/chem/img/MG.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/GH3.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/GH3.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | ChemComp-EDO / #4: Chemical | #5: Chemical | ChemComp-NA / | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 48.82 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / Details: PEG3350, sodium fluoride, Bis-Tris propane / PH range: 5.5-7.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 19, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.55→50 Å / Num. obs: 60205 / % possible obs: 98.5 % / Redundancy: 3.6 % / Net I/σ(I): 17.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4XJ1 Resolution: 1.552→46.997 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.46 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.552→46.997 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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