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Yorodumi- PDB-5aeo: Virulence-associated protein VapG from the intracellular pathogen... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5aeo | ||||||
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Title | Virulence-associated protein VapG from the intracellular pathogen Rhodococcus equi | ||||||
Components | R. EQUI VAPG PROTEIN | ||||||
Keywords | IMMUNE SYSTEM / BETA BARREL / BACTERIAL PATHOGEN / VIRULENCE PROTEIN / INTRACELLULAR PATHOGEN | ||||||
Function / homology | Function and homology information Rhodococcus equi virulence-associated protein / Rhodococcus equi virulence-associated protein / Rhodococcus equi virulence-associated superfamily / Rhodococcus equi virulence-associated protein / Lipocalin / Beta Barrel / Mainly Beta Similarity search - Domain/homology | ||||||
Biological species | RHODOCOCCUS EQUI (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Okoko, T. / Blagova, E.V. / Whittingham, J.L. / Dover, L.G. / Wilkinson, A.J. | ||||||
Citation | Journal: Vet.Microbiol. / Year: 2015 Title: Structural Characterisation of the Virulence-Associated Protein Vapg from the Horse Pathogen Rhodococcus Equi. Authors: Okoko, T. / Blagova, E.V. / Whittingham, J.L. / Dover, L.G. / Wilkinson, A.J. | ||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5aeo.cif.gz | 57.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5aeo.ent.gz | 41.2 KB | Display | PDB format |
PDBx/mmJSON format | 5aeo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5aeo_validation.pdf.gz | 437.8 KB | Display | wwPDB validaton report |
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Full document | 5aeo_full_validation.pdf.gz | 438.3 KB | Display | |
Data in XML | 5aeo_validation.xml.gz | 11.6 KB | Display | |
Data in CIF | 5aeo_validation.cif.gz | 15.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ae/5aeo ftp://data.pdbj.org/pub/pdb/validation_reports/ae/5aeo | HTTPS FTP |
-Related structure data
Related structure data | 4csbS S: Starting model for refinement |
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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 on special symmetry positions |
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-Components
#1: Protein | Mass: 17307.805 Da / Num. of mol.: 2 / Fragment: RESIDUES 27-172 Source method: isolated from a genetically manipulated source Source: (gene. exp.) RHODOCOCCUS EQUI (bacteria) / Strain: 103S / Plasmid: PET23B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9EU62, UniProt: A0A3S5Y0Q5*PLUS #2: Chemical | ChemComp-K / | #3: 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: 1.72 Å3/Da / Density % sol: 29 % / Description: NONE |
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Crystal grow | pH: 7.5 Details: PROTEIN SOLUTION: 30 MG/ML VAPG IN 10 MM TRIS-HCL PH 7.5, 10 MM NACL RESERVOIR: 0.3 M KCL, 20 % W/V PEG 3350 |
-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 |
Detector | Type: DECTRIS PIXEL / Detector: PIXEL / Date: Mar 17, 2013 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→31.5 Å / Num. obs: 24979 / % possible obs: 98 % / Redundancy: 11.4 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 31 |
Reflection shell | Resolution: 1.8→1.85 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.67 / Mean I/σ(I) obs: 2.6 / % possible all: 83 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4CSB Resolution: 1.8→31.5 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.937 / SU B: 2.943 / SU ML: 0.09 / Cross valid method: THROUGHOUT / ESU R: 0.118 / ESU R Free: 0.118 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. C-TERMINAL PEPTIDE FRAGMENTS IN MOLECULES A AND B VIOLATE CRYSTALLOGRAPHIC SYMMETRY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.009 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→31.5 Å
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Refine LS restraints |
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