+Open data
-Basic information
Entry | Database: PDB / ID: 3s8d | ||||||
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Title | Crystal Structure of RipA from Yersinia pestis | ||||||
Components | Coenzyme A transferase | ||||||
Keywords | TRANSFERASE / 4-HYDROXYBUTYRYL COA TRANSFERASE / COA TRANSFERASE | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Yersinia pestis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.31 Å | ||||||
Authors | Torres, R. / Goulding, C.W. | ||||||
Citation | Journal: Plos One / Year: 2011 Title: Biochemical, structural and molecular dynamics analyses of the potential virulence factor RipA from Yersinia pestis. Authors: Torres, R. / Swift, R.V. / Chim, N. / Wheatley, N. / Lan, B. / Atwood, B.R. / Pujol, C. / Sankaran, B. / Bliska, J.B. / Amaro, R.E. / Goulding, C.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3s8d.cif.gz | 171.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3s8d.ent.gz | 144.2 KB | Display | PDB format |
PDBx/mmJSON format | 3s8d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3s8d_validation.pdf.gz | 440.4 KB | Display | wwPDB validaton report |
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Full document | 3s8d_full_validation.pdf.gz | 457.3 KB | Display | |
Data in XML | 3s8d_validation.xml.gz | 33 KB | Display | |
Data in CIF | 3s8d_validation.cif.gz | 45.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/s8/3s8d ftp://data.pdbj.org/pub/pdb/validation_reports/s8/3s8d | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 50735.578 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Yersinia pestis (bacteria) / Gene: aCH1, y2385, YPO1926, YP_1668 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9ZC36 #2: 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: 2.36 Å3/Da / Density % sol: 47.92 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.7 Details: 18% PEG 3350, 0.2M sodium citrate, 0.1M Bis-tris propane, 1mM acetyl CoA, pH 5.7, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 200 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 21, 2009 |
Radiation | Protocol: SAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 2.3→50 Å / Num. obs: 38932 / % possible obs: 94.7 % / Biso Wilson estimate: 32.05 Å2 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.31→26.701 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7908 / SU ML: 0.6 / Cross valid method: FREE R / σ(F): 1 / Phase error: 28.19 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 23.502 Å2 / ksol: 0.33 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 94.95 Å2 / Biso mean: 39.5409 Å2 / Biso min: 17.47 Å2
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Refinement step | Cycle: LAST / Resolution: 2.31→26.701 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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