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Yorodumi- PDB-5cq9: Crystal structure of SopD2, a type III secreted virulence effecto... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5cq9 | ||||||
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Title | Crystal structure of SopD2, a type III secreted virulence effector from Salmonella enterica | ||||||
Components |
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Keywords | CELL INVASION / T3SS effector protein / Structural Genomics / Montreal-Kingston Bacterial Structural Genomics Initiative / BSGI | ||||||
Function / homology | Salmonella outer protein D / Salmonella outer protein D / protein secretion by the type III secretion system / host cell membrane / : / host cell plasma membrane / extracellular region / membrane / Secreted effector protein sopD2 Function and homology information | ||||||
Biological species | Salmonella typhimurium (bacteria) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å | ||||||
Authors | Shi, R. / Cygler, M. / Montreal-Kingston Bacterial Structural Genomics Initiative (BSGI) | ||||||
Funding support | Canada, 1items
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Citation | Journal: Cell Rep / Year: 2015 Title: Salmonella Disrupts Host Endocytic Trafficking by SopD2-Mediated Inhibition of Rab7. Authors: D'Costa, V.M. / Braun, V. / Landekic, M. / Shi, R. / Proteau, A. / McDonald, L. / Cygler, M. / Grinstein, S. / Brumell, J.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5cq9.cif.gz | 240.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5cq9.ent.gz | 196.9 KB | Display | PDB format |
PDBx/mmJSON format | 5cq9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5cq9_validation.pdf.gz | 448.3 KB | Display | wwPDB validaton report |
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Full document | 5cq9_full_validation.pdf.gz | 461.5 KB | Display | |
Data in XML | 5cq9_validation.xml.gz | 22.1 KB | Display | |
Data in CIF | 5cq9_validation.cif.gz | 29.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cq/5cq9 ftp://data.pdbj.org/pub/pdb/validation_reports/cq/5cq9 | HTTPS FTP |
-Related structure data
Related structure data | 5cpcSC 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 37832.027 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (bacteria) Strain: LT2 / SGSC1412 / ATCC 700720 / Gene: sopD2, STM0972 / Plasmid: pGEX-4T1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8ZQC8 #2: Protein/peptide | Mass: 954.168 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria) Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Sequence details | Author believes that chain C and chain D are part of the SopD2 protein. They are built based on the ...Author believes that chain C and chain D are part of the SopD2 protein. They are built based on the electron density maps but the side chains of these two segments are not clear due to the poor quality of the maps therefore residues identity can not be assigned unambiguously. Very likely these are part of the flexible N-terminal (residues 1-35) segment, i.e., chain C is part of the N-terminal of chain A and chain D is part of the N-terminal of chain B. | |
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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: 2.76 Å3/Da / Density % sol: 55.44 % |
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Crystal grow | Temperature: 295 K / Method: microbatch / pH: 9.5 / Details: 0.1M CHES pH 9.5, 20% PEG 8000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.9795 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Aug 10, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 3→50 Å / Num. obs: 16873 / % possible obs: 99.8 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.059 / Net I/σ(I): 12.8 |
Reflection shell | Resolution: 3→3.11 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.739 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5CPC Resolution: 3→50 Å / SU B: 62.231 / SU ML: 0.498 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.506 Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Displacement parameters | Biso mean: 86.56 Å2
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Refinement step | Cycle: LAST / Resolution: 3→50 Å
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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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