+Open data
-Basic information
Entry | Database: PDB / ID: 3hw2 | ||||||
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Title | Crystal structure of the SifA-SKIP(PH) complex | ||||||
Components |
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Keywords | SIGNALING PROTEIN / sifa / protein complex / salmonella infection / late effector / Virulence / Phosphoprotein | ||||||
Function / homology | Function and homology information symbiont-mediated perturbation of host small GTPase-mediated signal transduction / symbiont-mediated perturbation of host microtubule cytoskeleton / lysosome localization / natural killer cell mediated cytotoxicity / Golgi organization / kinesin binding / regulation of protein localization / host cell cytoplasm / endosome membrane / lysosomal membrane ...symbiont-mediated perturbation of host small GTPase-mediated signal transduction / symbiont-mediated perturbation of host microtubule cytoskeleton / lysosome localization / natural killer cell mediated cytotoxicity / Golgi organization / kinesin binding / regulation of protein localization / host cell cytoplasm / endosome membrane / lysosomal membrane / host cell plasma membrane / extracellular region / membrane Similarity search - Function | ||||||
Biological species | Salmonella enterica subsp. enterica serovar Typhimurium (bacteria) Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å | ||||||
Authors | Diacovich, L. / Dumont, A. / Lafitte, D. / Soprano, E. / Guilhon, A.-A. / Bignon, C. / Gorvel, J.-P. / Bourne, Y. / Meresse, S. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2009 Title: Interaction between the SifA virulence factor and its host target skip is essential for salmonella pathogenesis Authors: Diacovich, L. / Dumont, A. / Lafitte, D. / Soprano, E. / Guilhon, A.-A. / Bignon, C. / Gorvel, J.-P. / Bourne, Y. / Meresse, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3hw2.cif.gz | 93.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3hw2.ent.gz | 71.2 KB | Display | PDB format |
PDBx/mmJSON format | 3hw2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3hw2_validation.pdf.gz | 435.8 KB | Display | wwPDB validaton report |
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Full document | 3hw2_full_validation.pdf.gz | 445 KB | Display | |
Data in XML | 3hw2_validation.xml.gz | 17.2 KB | Display | |
Data in CIF | 3hw2_validation.cif.gz | 22.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hw/3hw2 ftp://data.pdbj.org/pub/pdb/validation_reports/hw/3hw2 | HTTPS FTP |
-Related structure data
Related structure data | 3cxbS 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: 38546.340 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria) Plasmid: pDEST14 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q56061 |
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#2: Protein | Mass: 11734.374 Da / Num. of mol.: 1 Fragment: Pleskrin homology (PH) domain, UNP residues 771-876 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pDEST14 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q8IWE5 |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.24 Å3/Da / Density % sol: 45.1 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 30% PEG 4000, 0.2M Na acetate trihydrate, 0.1 M Tris-HCl, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.939 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 6, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.939 Å / Relative weight: 1 |
Reflection | Resolution: 3.3→20 Å / Num. obs: 7176 / % possible obs: 99.3 % / Redundancy: 4.4 % / Rsym value: 0.091 / Net I/σ(I): 8.9 / Num. measured all: 31607 |
Reflection shell | Resolution: 3.3→3.4 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 3 / Rsym value: 0.41 / % possible all: 95.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3CXB Resolution: 3.3→20 Å / Cor.coef. Fo:Fc: 0.913 / Cor.coef. Fo:Fc free: 0.863 / SU B: 96.209 / SU ML: 0.694 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.76 / 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: 50.438 Å2
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Refinement step | Cycle: LAST / Resolution: 3.3→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.3→3.384 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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