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Yorodumi- PDB-5jbs: Conformational changes during monomer-to-dimer transition of Bruc... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5jbs | ||||||
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Title | Conformational changes during monomer-to-dimer transition of Brucella suis VirB8 | ||||||
Components | Type IV secretion system protein virB8 | ||||||
Keywords | TRANSPORT PROTEIN / M012R-VirB8 | ||||||
Function / homology | Function and homology information protein secretion by the type IV secretion system / identical protein binding / plasma membrane Similarity search - Function | ||||||
Biological species | Brucella suis biovar 1 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å | ||||||
Authors | Arya, T. / Sharifahmadian, M. / Sygusch, J. / Baron, B. | ||||||
Funding support | Canada, 1items
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Citation | Journal: To Be Published Title: NMR analyses, X-ray crystallography and small-molecule probing reveal conformational shifts during monomer-to-dimer transition of Brucella suis VirB8 Authors: Arya, T. / Sharifahmadian, M. / Sygusch, J. / Baron, B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5jbs.cif.gz | 126 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5jbs.ent.gz | 98.1 KB | Display | PDB format |
PDBx/mmJSON format | 5jbs.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5jbs_validation.pdf.gz | 488.3 KB | Display | wwPDB validaton report |
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Full document | 5jbs_full_validation.pdf.gz | 502.2 KB | Display | |
Data in XML | 5jbs_validation.xml.gz | 27.6 KB | Display | |
Data in CIF | 5jbs_validation.cif.gz | 37.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jb/5jbs ftp://data.pdbj.org/pub/pdb/validation_reports/jb/5jbs | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 15948.614 Da / Num. of mol.: 4 / Mutation: M102R Source method: isolated from a genetically manipulated source Source: (gene. exp.) Brucella suis biovar 1 (strain 1330) (bacteria) Strain: 1330 / Gene: virB8, BRA0062, BS1330_II0062 / Production host: Escherichia coli (E. coli) / References: UniProt: Q7CEG3 |
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-Non-polymers , 5 types, 332 molecules
#2: Chemical | #3: Chemical | ChemComp-GOL / | #4: Chemical | ChemComp-PEG / #5: Chemical | #6: 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: 2.95 Å3/Da / Density % sol: 58.35 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.8 / Details: 0.1 M Tris/HCl pH 6.8, 18% PEG-MME 2000 / PH range: 6.6-7.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 2, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→42.2 Å / Num. obs: 48835 / % possible obs: 97 % / Redundancy: 3.5 % / Net I/σ(I): 2.4 |
-Processing
Software | Name: REFMAC / Version: 5.8.0123 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→42.2 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.936 / SU B: 5.374 / SU ML: 0.142 / Cross valid method: THROUGHOUT / ESU R: 0.155 / ESU R Free: 0.152 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 47.119 Å2
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Refinement step | Cycle: LAST / Resolution: 1.95→42.2 Å
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Refine LS restraints |
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