+Open data
-Basic information
Entry | Database: PDB / ID: 5lq7 | |||||||||
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Title | Salmonella effector SpvD - G161 variant | |||||||||
Components | Virulence protein vsdE | |||||||||
Keywords | IMMUNOSUPPRESSANT / Effector / signaling protein | |||||||||
Function / homology | Salmonella plasmid virulence SpvD / Salmonella plasmid virulence protein SpvD / DI(HYDROXYETHYL)ETHER / Virulence protein vsdE Function and homology information | |||||||||
Biological species | Salmonella enterica (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | |||||||||
Authors | Przydacz, M. / Grabe, G.J. / Holden, D.W. / Hare, S.A. | |||||||||
Funding support | United Kingdom, 1items
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Citation | Journal: J. Biol. Chem. / Year: 2016 Title: The Salmonella Effector SpvD Is a Cysteine Hydrolase with a Serovar-specific Polymorphism Influencing Catalytic Activity, Suppression of Immune Responses, and Bacterial Virulence. Authors: Grabe, G.J. / Zhang, Y. / Przydacz, M. / Rolhion, N. / Yang, Y. / Pruneda, J.N. / Komander, D. / Holden, D.W. / Hare, S.A. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5lq7.cif.gz | 64 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5lq7.ent.gz | 44.8 KB | Display | PDB format |
PDBx/mmJSON format | 5lq7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5lq7_validation.pdf.gz | 456.1 KB | Display | wwPDB validaton report |
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Full document | 5lq7_full_validation.pdf.gz | 456.4 KB | Display | |
Data in XML | 5lq7_validation.xml.gz | 12.1 KB | Display | |
Data in CIF | 5lq7_validation.cif.gz | 17.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lq/5lq7 ftp://data.pdbj.org/pub/pdb/validation_reports/lq/5lq7 | HTTPS FTP |
-Related structure data
Related structure data | 5lq6SC S: Starting model for refinement C: citing same article (ref.) |
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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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 24893.734 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Salmonella enterica (bacteria) / Gene: vsdE, spvD, PSLT037 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A2N2 |
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-Non-polymers , 5 types, 210 molecules
#2: Chemical | ChemComp-TRS / | ||||
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#3: Chemical | ChemComp-PEG / | ||||
#4: Chemical | #5: Chemical | ChemComp-CL / | #6: 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: 2.07 Å3/Da / Density % sol: 40.47 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 100 mM Tris, 200 mM NaCl, 22 % PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.97949 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 12, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97949 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→51.97 Å / Num. obs: 26737 / % possible obs: 99.4 % / Redundancy: 5.9 % / Rmerge(I) obs: 0.104 / Net I/σ(I): 10.4 |
Reflection shell | Resolution: 1.6→1.69 Å / Redundancy: 6 % / Mean I/σ(I) obs: 1.9 / CC1/2: 0.579 / % possible all: 99.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5LQ6 Resolution: 1.6→44.98 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.954 / SU B: 2.105 / SU ML: 0.071 / Cross valid method: THROUGHOUT / ESU R: 0.088 / ESU R Free: 0.089 / 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: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.415 Å2
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Refinement step | Cycle: 1 / Resolution: 1.6→44.98 Å
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Refine LS restraints |
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