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Yorodumi- PDB-4xj5: Crystal structure of Vibrio cholerae DncV 3'-deoxy GTP bound form -
+Open data
-Basic information
Entry | Database: PDB / ID: 4xj5 | ||||||
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Title | Crystal structure of Vibrio cholerae DncV 3'-deoxy GTP bound form | ||||||
Components | Cyclic AMP-GMP synthase | ||||||
Keywords | TRANSFERASE / Cyclic GMP-AMP synthase / Bacterial virulence / nucleotidyltransferase | ||||||
Function / homology | Function and homology information 3',3'-cyclic GMP-AMP synthase activity / cyclic nucleotide biosynthetic process / diguanylate cyclase activity / negative regulation of chemotaxis / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / defense response to virus / GTP binding / ATP binding / metal ion binding Similarity search - Function | ||||||
Biological species | Vibrio cholerae O1 biovar El Tor str. N16961 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.552 Å | ||||||
Authors | Kato, K. / Ishii, R. / Ishitani, R. / Nureki, O. | ||||||
Citation | Journal: Structure / Year: 2015 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4xj5.cif.gz | 172.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4xj5.ent.gz | 134.5 KB | Display | PDB format |
PDBx/mmJSON format | 4xj5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xj/4xj5 ftp://data.pdbj.org/pub/pdb/validation_reports/xj/4xj5 | HTTPS FTP |
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-Related structure data
Related structure data | 4xj1SC 4xj3C 4xj4C 4xj6C 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
-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.) Vibrio cholerae O1 biovar El Tor str. N16961 (bacteria) Strain: N16961 / Gene: dncV, VC_0179 / Production host: Escherichia coli (E. coli) References: UniProt: Q9KVG7, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases |
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-Non-polymers , 5 types, 255 molecules
#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: X-RAY DIFFRACTION |
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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: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å |
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 |
-Processing
Software |
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Refinement | Method to determine structure: SAD 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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