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Yorodumi- PDB-3w30: Structual basis for the recognition of Ubc13 by the Shigella flex... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3w30 | ||||||
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Title | Structual basis for the recognition of Ubc13 by the Shigella flexneri effector OspI | ||||||
Components | ORF169b | ||||||
Keywords | IMMUNE SYSTEM / Type 3 secretion system / Effector / Deamidation | ||||||
Function / homology | Cathepsin B; Chain A - #140 / : / : / Shigella glutamine deamidase OspI / Cathepsin B; Chain A / Alpha-Beta Complex / Alpha Beta / ORF169b Function and homology information | ||||||
Biological species | Shigella flexneri (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.99 Å | ||||||
Authors | Nishide, A. / Kim, M. / Takagi, K. / Sasakawa, C. / Mizushima, T. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2013 Title: Structural Basis for the Recognition of Ubc13 by the Shigella flexneri Effector OspI. Authors: Nishide, A. / Kim, M. / Takagi, K. / Himeno, A. / Sanada, T. / Sasakawa, C. / Mizushima, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3w30.cif.gz | 83.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3w30.ent.gz | 63.7 KB | Display | PDB format |
PDBx/mmJSON format | 3w30.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3w30_validation.pdf.gz | 442.9 KB | Display | wwPDB validaton report |
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Full document | 3w30_full_validation.pdf.gz | 449.3 KB | Display | |
Data in XML | 3w30_validation.xml.gz | 15.4 KB | Display | |
Data in CIF | 3w30_validation.cif.gz | 20.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w3/3w30 ftp://data.pdbj.org/pub/pdb/validation_reports/w3/3w30 | HTTPS FTP |
-Related structure data
Related structure data | 3w31C 3b21S C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 24118.807 Da / Num. of mol.: 2 / Mutation: C62A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Shigella flexneri (bacteria) / Gene: ORF169b, CP0209 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8VSD5 |
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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: 2.01 Å3/Da / Density % sol: 38.91 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.2M Magnesium Acetate, 0.1M Tris-HCl (pH6.5), 25% (w/v) PEG 8000, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å |
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Detector | Date: Jan 1, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 2.99→50 Å / Num. obs: 8233 / % possible obs: 100 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.141 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3B21 Resolution: 2.99→30 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.876 / SU B: 20.272 / SU ML: 0.387 / Cross valid method: THROUGHOUT / ESU R Free: 0.572 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 10.794 Å2
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Refinement step | Cycle: LAST / Resolution: 2.99→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.989→3.066 Å / Total num. of bins used: 20
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