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- PDB-5cq9: Crystal structure of SopD2, a type III secreted virulence effecto... -

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Basic information

Entry
Database: PDB / ID: 5cq9
TitleCrystal structure of SopD2, a type III secreted virulence effector from Salmonella enterica
Components
  • 11-mer peptide
  • Secreted effector protein sopD2
KeywordsCELL INVASION / T3SS effector protein / Structural Genomics / Montreal-Kingston Bacterial Structural Genomics Initiative / BSGI
Function / homologySalmonella 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 speciesSalmonella typhimurium (bacteria)
Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsShi, R. / Cygler, M. / Montreal-Kingston Bacterial Structural Genomics Initiative (BSGI)
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)GSP-48370 Canada
CitationJournal: 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
DepositionJul 21, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 9, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 16, 2015Group: Database references
Revision 1.2Sep 13, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Secreted effector protein sopD2
B: Secreted effector protein sopD2
C: 11-mer peptide
D: 11-mer peptide


Theoretical massNumber of molelcules
Total (without water)77,5724
Polymers77,5724
Non-polymers00
Water00
1
A: Secreted effector protein sopD2
C: 11-mer peptide


Theoretical massNumber of molelcules
Total (without water)38,7862
Polymers38,7862
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Secreted effector protein sopD2
D: 11-mer peptide


Theoretical massNumber of molelcules
Total (without water)38,7862
Polymers38,7862
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.613, 89.800, 75.595
Angle α, β, γ (deg.)90.00, 117.15, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Secreted effector protein sopD2 / Salmonella outer protein D 2


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 11-mer 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)
Has protein modificationY
Sequence detailsAuthor 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

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.76 Å3/Da / Density % sol: 55.44 %
Crystal growTemperature: 295 K / Method: microbatch / pH: 9.5 / Details: 0.1M CHES pH 9.5, 20% PEG 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.9795 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Aug 10, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 3→3.11 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.739 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
HKL-2000data scaling
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5CPC

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
RfactorNum. reflection% reflectionSelection details
Rfree0.309 850 5 %RANDOM
Rwork0.235 ---
obs0.239 15983 99.4 %-
Displacement parametersBiso mean: 86.56 Å2
Baniso -1Baniso -2Baniso -3
1-4.79 Å20 Å2-4.04 Å2
2--0.47 Å20 Å2
3----0.74 Å2
Refinement stepCycle: LAST / Resolution: 3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4577 0 0 0 4577
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.8330.40320.35832.39641.19871.2393-0.1105-0.03810.1305-0.2485-0.02960.0369-0.0947-0.14270.14010.03640.0018-0.01330.06870.00740.147921.16111.34110.7862
20.53790.82581.03791.52951.38153.47940.04860.0322-0.01380.12590.0261-0.02980.05130.0236-0.07470.0189-0.01750.01670.0822-0.04160.11853.0757-67.1558-22.4053
31.0592-0.5636-0.28640.39130.15170.1255-0.3914-0.3761-0.11510.30110.2613-0.16620.15330.1940.13010.6693-0.04340.03770.6487-0.0370.816920.6949-34.9487-14.4469
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A76 - 319
2X-RAY DIFFRACTION2B76 - 319
3X-RAY DIFFRACTION3A36 - 62
4X-RAY DIFFRACTION3B36 - 63
5X-RAY DIFFRACTION3D15 - 25
6X-RAY DIFFRACTION3C16 - 24

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