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Yorodumi- PDB-3l3p: Crystal structure of the C-terminal domain of Shigella type III e... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3l3p | ||||||
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Title | Crystal structure of the C-terminal domain of Shigella type III effector IpaH9.8, with a novel domain swap | ||||||
Components | IpaH9.8 | ||||||
Keywords | LIGASE / E3 ligase / Domain swap / CXD motif | ||||||
Function / homology | Function and homology information symbiont-mediated perturbation of host NF-kappaB cascade / symbiont-mediated suppression of host inflammatory response / symbiont-mediated suppression of host defenses / symbiont-mediated suppression of host NF-kappaB cascade / protein K27-linked ubiquitination / symbiont-mediated suppression of host innate immune response / host cell cytosol / : / protein autoubiquitination / protein K48-linked ubiquitination ...symbiont-mediated perturbation of host NF-kappaB cascade / symbiont-mediated suppression of host inflammatory response / symbiont-mediated suppression of host defenses / symbiont-mediated suppression of host NF-kappaB cascade / protein K27-linked ubiquitination / symbiont-mediated suppression of host innate immune response / host cell cytosol / : / protein autoubiquitination / protein K48-linked ubiquitination / RING-type E3 ubiquitin transferase / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / host cell nucleus / extracellular region / identical protein binding Similarity search - Function | ||||||
Biological species | Shigella flexneri (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å | ||||||
Authors | Seyedarabi, A. / Sullivan, J.A. / Sasakawa, C. / Pickersgill, R.W. | ||||||
Citation | Journal: Febs Lett. / Year: 2010 Title: A disulfide driven domain swap switches off the activity of Shigella IpaH9.8 E3 ligase Authors: Seyedarabi, A. / Sullivan, J.A. / Sasakawa, C. / Pickersgill, R.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3l3p.cif.gz | 62.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3l3p.ent.gz | 46.1 KB | Display | PDB format |
PDBx/mmJSON format | 3l3p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3l3p_validation.pdf.gz | 431.1 KB | Display | wwPDB validaton report |
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Full document | 3l3p_full_validation.pdf.gz | 432.9 KB | Display | |
Data in XML | 3l3p_validation.xml.gz | 10.6 KB | Display | |
Data in CIF | 3l3p_validation.cif.gz | 13.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l3/3l3p ftp://data.pdbj.org/pub/pdb/validation_reports/l3/3l3p | HTTPS FTP |
-Related structure data
Related structure data | 3ckdS S: Starting model for refinement |
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Similar 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: 33460.027 Da / Num. of mol.: 1 Fragment: C-terminal domain (domain swapped), residues 254-545 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Shigella flexneri (bacteria) / Strain: YSH6000 / Gene: ipaH9.8 / Plasmid: pET14b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: O85159, UniProt: Q8VSC3*PLUS, ubiquitin-protein ligase |
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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: 2.51 Å3/Da / Density % sol: 51.02 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 0.2M sodium acetate trihydrate, 0.1M Tris pH 8.5, 30% polyethylene glycol, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX10.1 / Wavelength: 1.04496 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 23, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.04496 Å / Relative weight: 1 |
Reflection | Resolution: 3.2→38.46 Å / Num. all: 6131 / Num. obs: 5984 / % possible obs: 97.6 % / Redundancy: 9.1 % / Biso Wilson estimate: 75.8 Å2 / Rmerge(I) obs: 0.083 / Rsym value: 0.083 / Net I/σ(I): 21.7 |
Reflection shell | Resolution: 3.2→3.37 Å / Redundancy: 9.2 % / Rmerge(I) obs: 0.53 / Mean I/σ(I) obs: 4.2 / Num. unique all: 785 / Rsym value: 0.53 / % possible all: 91.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3ckd; chain A Resolution: 3.2→34.53 Å / Cor.coef. Fo:Fc: 0.897 / Cor.coef. Fo:Fc free: 0.923 / SU B: 35.258 / SU ML: 0.562 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R Free: 0.62 / 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: 85.882 Å2
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Refinement step | Cycle: LAST / Resolution: 3.2→34.53 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.2→3.283 Å / Total num. of bins used: 20
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