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Yorodumi- PDB-4o7k: Crystal structure of Oncogenic Suppression Activity Protein - A P... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4o7k | ||||||
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Title | Crystal structure of Oncogenic Suppression Activity Protein - A Plasmid Fertility Inhibition Factor | ||||||
Components | Protein osa | ||||||
Keywords | ANTITUMOR PROTEIN / Plasmid Fertility Inhibition | ||||||
Function / homology | FiwA/Osa / ISOPROPYL ALCOHOL / PHOSPHATE ION / Protein osa Function and homology information | ||||||
Biological species | Shigella flexneri (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SIRAS / Resolution: 1.748 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 | 4o7k.cif.gz | 54.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4o7k.ent.gz | 39.4 KB | Display | PDB format |
PDBx/mmJSON format | 4o7k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4o7k_validation.pdf.gz | 442.1 KB | Display | wwPDB validaton report |
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Full document | 4o7k_full_validation.pdf.gz | 442.6 KB | Display | |
Data in XML | 4o7k_validation.xml.gz | 10.3 KB | Display | |
Data in CIF | 4o7k_validation.cif.gz | 13.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o7/4o7k ftp://data.pdbj.org/pub/pdb/validation_reports/o7/4o7k | 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: 21277.684 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-CL / | #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: 2.76 Å3/Da / Density % sol: 55.47 % |
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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: 1.748→50 Å / Num. all: 25018 / Num. obs: 24068 / % possible obs: 96.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 25.8 % / Biso Wilson estimate: 28.01 Å2 / Rmerge(I) obs: 0.057 |
Reflection shell | Resolution: 1.748→1.81 Å / Rmerge(I) obs: 0.433 / % possible all: 80.1 |
-Processing
Software |
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Refinement | Method to determine structure: SIRAS / Resolution: 1.748→25.537 Å / FOM work R set: 0.7847 / SU ML: 0.22 / σ(F): 1.41 / Phase error: 25.77 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 84.6 Å2 / Biso mean: 35.19 Å2 / Biso min: 19.78 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.748→25.537 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: 9
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