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Yorodumi- PDB-4dvc: Structural and functional studies of TcpG, the Vibrio cholerae Ds... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4dvc | ||||||
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Title | Structural and functional studies of TcpG, the Vibrio cholerae DsbA disulfide-forming protein required for pilus and cholera toxin production | ||||||
Components | Thiol:disulfide interchange protein DsbA | ||||||
Keywords | OXIDOREDUCTASE / Cholera / pilus assembly / Thioredoxin fold / DsbA-like / Disulfide bond / DsbB | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Vibrio cholerae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.2 Å | ||||||
Authors | Walden, P.M. / Martin, J.L. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2012 Title: The 1.2 A resolution crystal structure of TcpG, the Vibrio cholerae DsbA disulfide-forming protein required for pilus and cholera-toxin production Authors: Walden, P.M. / Heras, B. / Chen, K.-E. / Halili, M.A. / Rimmer, K. / Sharma, P. / Scanlon, M.J. / Martin, J.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4dvc.cif.gz | 127.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4dvc.ent.gz | 108 KB | Display | PDB format |
PDBx/mmJSON format | 4dvc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4dvc_validation.pdf.gz | 429.7 KB | Display | wwPDB validaton report |
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Full document | 4dvc_full_validation.pdf.gz | 429.7 KB | Display | |
Data in XML | 4dvc_validation.xml.gz | 11.8 KB | Display | |
Data in CIF | 4dvc_validation.cif.gz | 17.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dv/4dvc ftp://data.pdbj.org/pub/pdb/validation_reports/dv/4dvc | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 20748.580 Da / Num. of mol.: 1 / Fragment: UNP residues 19-200 / Mutation: R134H, V164A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vibrio cholerae (bacteria) / Strain: serotype O1 (ATCC 39315 / El Tor Inaba N16961) / Gene: tpcG / Plasmid: pET-21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P32557 | ||||||
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#2: Chemical | #3: Chemical | ChemComp-SO4 / | #4: Water | ChemComp-HOH / | Sequence details | THIS SEQUENCE CONFLICT IS BASED ON REFERENCE 1 OF DATABASE UNIPROTKB/SWISS-PROT P32557 (DSBA_VIBCH). | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.17 Å3/Da / Density % sol: 43.36 % |
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Crystal grow | Temperature: 277.15 K / Method: hanging drop / pH: 6.4 Details: PEG 4000, MES, pH 6.4, hanging drop, temperature 277.15K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9536 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 9, 2009 |
Radiation | Monochromator: Sagitally focussed Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9536 Å / Relative weight: 1 |
Reflection | Resolution: 1.2→64.2 Å / Num. obs: 56644 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 14 % / Biso Wilson estimate: 10 Å2 / Rmerge(I) obs: 0.103 / Net I/σ(I): 18 |
Reflection shell | Highest resolution: 1.2 Å / Redundancy: 12.9 % / Rmerge(I) obs: 0.103 / Mean I/σ(I) obs: 3.1 / % possible all: 97.4 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.2→32.132 Å / Occupancy max: 1 / Occupancy min: 0 / SU ML: 0.09 / σ(F): 1.34 / Phase error: 11.33 / Stereochemistry target values: MLHL
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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: 16.3622 Å2
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Refinement step | Cycle: LAST / Resolution: 1.2→32.132 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14
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