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Open data
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Basic information
Entry | Database: PDB / ID: 3b21 | ||||||
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Title | Crystal structure of OspI from Shigella flexineri | ||||||
![]() | ORF169b | ||||||
![]() | UNKNOWN FUNCTION / Shigella / Bacterial protein / effector / type 3 secretion system | ||||||
Function / homology | Cathepsin B; Chain A - #140 / : / : / Shigella glutamine deamidase OspI / Cathepsin B; Chain A / Alpha-Beta Complex / Alpha Beta / ORF169b![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Sanada, T. / Kim, M. / Sasakawa, C. / Mizushima, T. | ||||||
![]() | ![]() Title: The Shigella flexneri effector OspI deamidates UBC13 to dampen the inflammatory response Authors: Sanada, T. / Kim, M. / Mimuro, H. / Suzuki, M. / Ogawa, M. / Oyama, A. / Ashida, H. / Kobayashi, T. / Koyama, T. / Nagai, S. / Shibata, Y. / Gohda, J. / Inoue, J.I. / Mizushima, T. / Sasakawa, C. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 48.9 KB | Display | ![]() |
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PDB format | ![]() | 37.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 417.1 KB | Display | ![]() |
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Full document | ![]() | 419.6 KB | Display | |
Data in XML | ![]() | 10.3 KB | Display | |
Data in CIF | ![]() | 14 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 24150.873 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 44.18 % |
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Crystal grow | Temperature: 288 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.1M MES, 0.1M NaAcetate, 1.0M NaCl, 24%(w/v) PEG 8000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 288K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: Bruker DIP-6040 / Detector: CCD / Date: Dec 13, 2007 |
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→50 Å / Num. obs: 14220 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 6 % / Rmerge(I) obs: 0.098 / Net I/σ(I): 13.1 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 6 % / Rmerge(I) obs: 0.35 / % possible all: 99.9 |
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Processing
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Refinement | Method to determine structure: ![]()
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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: 16.513 Å2
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Refinement step | Cycle: LAST / Resolution: 2.01→45.62 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.008→2.06 Å / Total num. of bins used: 20
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