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Yorodumi- PDB-4u03: Structure of the vibrio cholerae di-nucleotide cyclase (DncV) in ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4u03 | |||||||||
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Title | Structure of the vibrio cholerae di-nucleotide cyclase (DncV) in complex with GTP and 5MTHFGLU2 | |||||||||
Components | Cyclic AMP-GMP synthase | |||||||||
Keywords | TRANSFERASE / regulation | |||||||||
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 El Tor N16961 (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.041 Å | |||||||||
Authors | Zhu, D.Y. / Xiang, Y. | |||||||||
Funding support | China, 2items
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Citation | Journal: Mol.Cell / Year: 2014 Title: Structural Biochemistry of a Vibrio cholerae Dinucleotide Cyclase Reveals Cyclase Activity Regulation by Folates. Authors: Zhu, D. / Wang, L. / Shang, G. / Liu, X. / Zhu, J. / Lu, D. / Wang, L. / Kan, B. / Zhang, J.R. / Xiang, Y. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4u03.cif.gz | 347.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4u03.ent.gz | 281.7 KB | Display | PDB format |
PDBx/mmJSON format | 4u03.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4u03_validation.pdf.gz | 2 MB | Display | wwPDB validaton report |
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Full document | 4u03_full_validation.pdf.gz | 2 MB | Display | |
Data in XML | 4u03_validation.xml.gz | 34.1 KB | Display | |
Data in CIF | 4u03_validation.cif.gz | 47.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u0/4u03 ftp://data.pdbj.org/pub/pdb/validation_reports/u0/4u03 | HTTPS FTP |
-Related structure data
Related structure data | 4u0lSC 4u0mC 4u0nC 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 48825.398 Da / Num. of mol.: 2 / Fragment: UNP residues 1-419 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vibrio cholerae El Tor N16961 (bacteria) Gene: dncV, VC_0179 / Plasmid: PET22B / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9KVG7, cyclic GMP-AMP synthase #2: Chemical | ChemComp-GTP / #3: Chemical | ChemComp-MG / #4: Chemical | #5: Water | ChemComp-HOH / | |
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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: 2.21 Å3/Da / Density % sol: 44.31 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 20% w/v PEG 3350, 200mM NaCl, 5mM ATP, 5mM GTP |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.968 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: May 20, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.968 Å / Relative weight: 1 |
Reflection | Resolution: 2.04→103 Å / Num. obs: 54229 / % possible obs: 99 % / Redundancy: 3.6 % / Net I/σ(I): 16.9 |
-Processing
Software | Name: PHENIX / Version: (phenix.refine: 1.8.2_1309) / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4U0L Resolution: 2.041→43.633 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.83 / 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: 2.041→43.633 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 64.2877 Å / Origin y: 8.5722 Å / Origin z: 176.361 Å
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Refinement TLS group | Selection details: all |