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Yorodumi- PDB-4ovb: Crystal structure of Oncogenic Suppression Activity Protein - A P... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4ovb | ||||||
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Title | Crystal structure of Oncogenic Suppression Activity Protein - A Plasmid Fertility Inhibition Factor, Gold (I) Cyanide derivative | ||||||
Components | Protein osa | ||||||
Keywords | ANTITUMOR PROTEIN / Plasmid Fertility Inhibition | ||||||
Function / homology | FiwA/Osa / : / Plasmid Fertility inhibition factor / GOLD (I) CYANIDE ION / PHOSPHATE ION / Protein osa Function and homology information | ||||||
Biological species | Shigella flexneri (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SIRAS / Resolution: 2.034 Å | ||||||
Authors | Maindola, P. / Goyal, P. / Arulandu, A. | ||||||
Citation | Journal: Nat Commun / Year: 2014 Title: Multiple enzymatic activities of ParB/Srx superfamily mediate sexual conflict among conjugative plasmids Authors: Maindola, P. / Raina, R. / Goyal, P. / Atmakuri, K. / Ojha, A. / Gupta, S. / Christie, P.J. / Iyer, L.M. / Aravind, L. / Arockiasamy, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ovb.cif.gz | 53.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ovb.ent.gz | 38.1 KB | Display | PDB format |
PDBx/mmJSON format | 4ovb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4ovb_validation.pdf.gz | 450.8 KB | Display | wwPDB validaton report |
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Full document | 4ovb_full_validation.pdf.gz | 451.1 KB | Display | |
Data in XML | 4ovb_validation.xml.gz | 10.5 KB | Display | |
Data in CIF | 4ovb_validation.cif.gz | 14.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ov/4ovb ftp://data.pdbj.org/pub/pdb/validation_reports/ov/4ovb | 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: 21001.391 Da / Num. of mol.: 1 / Mutation: R4W Source method: isolated from a genetically manipulated source Details: IncW plasmid Sa (pSa) / Source: (gene. exp.) Shigella flexneri (bacteria) / Gene: osa / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P29772 | ||||||
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#2: Chemical | #3: Chemical | ChemComp-AUC / #4: Chemical | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.81 Å3/Da / Density % sol: 56.25 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 4.2 Details: 10% Isopropanol, 0.5M lithium sulphate, 0.1M phosphate-citrate buffer pH 4.2, 0.2M NDSB-201, VAPOR DIFFUSION, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Aug 31, 2007 / Details: VariMax |
Radiation | Monochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.03→50 Å / Num. all: 16254 / Num. obs: 15539 / % possible obs: 95.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 46.2 % / Rmerge(I) obs: 0.071 / Net I/σ(I): 61.21 |
Reflection shell | Resolution: 2.03→2.1 Å / Redundancy: 23.3 % / Rmerge(I) obs: 0.548 / % possible all: 85.1 |
-Processing
Software |
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Refinement | Method to determine structure: SIRAS / Resolution: 2.034→27.49 Å / SU ML: 0.2 / σ(F): 1.38 / Phase error: 25.04 / 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: 2.034→27.49 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: 6
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