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- PDB-5cpc: Crystal structure of SopD, a type III secreted virulence effector... -

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Basic information

Entry
Database: PDB / ID: 5cpc
TitleCrystal structure of SopD, a type III secreted virulence effector from Salmonella enterica
ComponentsSecreted effector protein SopD
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 cytosol / host cell membrane / host cell plasma membrane / extracellular region / membrane / Secreted effector protein SopD
Function and homology information
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.15 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 1.4Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Secreted effector protein SopD
B: Secreted effector protein SopD


Theoretical massNumber of molelcules
Total (without water)72,3762
Polymers72,3762
Non-polymers00
Water1,964109
1
A: Secreted effector protein SopD


Theoretical massNumber of molelcules
Total (without water)36,1881
Polymers36,1881
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Secreted effector protein SopD


Theoretical massNumber of molelcules
Total (without water)36,1881
Polymers36,1881
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.525, 102.743, 76.018
Angle α, β, γ (deg.)90.000, 105.530, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Secreted effector protein SopD / Salmonella outer protein D


Mass: 36188.223 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: sopD, STM2945 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P40722
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 109 / Source method: isolated from a natural source / Formula: H2O

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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: 2.42 Å3/Da / Density % sol: 49.15 %
Crystal growTemperature: 295 K / Method: microbatch / pH: 7 / Details: 0.1M HEPES pH 7, 20% PEG 6000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9793 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jul 10, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.15→50 Å / Num. obs: 37360 / % possible obs: 99 % / Redundancy: 7.5 % / Rmerge(I) obs: 0.064 / Χ2: 2.245 / Net I/av σ(I): 54.3 / Net I/σ(I): 17.4 / Num. measured all: 280209
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.15-2.237.60.52137611.218100
2.23-2.327.60.3937451.245100
2.32-2.427.70.25737581.249100
2.42-2.557.70.18337461.352100
2.55-2.717.70.12637781.475100
2.71-2.927.70.08637711.663100
2.92-3.217.70.07137562.358100
3.21-3.687.20.06537854.091100
3.68-4.636.90.05737664.8199.8
4.63-507.20.04534943.57290.7

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Processing

Software
NameVersionClassification
HKL-2000data scaling
REFMAC5.5.0109refinement
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
SHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 2.15→50 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.941 / WRfactor Rfree: 0.2555 / WRfactor Rwork: 0.2225 / FOM work R set: 0.8022 / SU B: 14.162 / SU ML: 0.162 / SU R Cruickshank DPI: 0.2405 / SU Rfree: 0.1916 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.24 / ESU R Free: 0.192 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2434 1867 5 %RANDOM
Rwork0.2122 ---
obs0.2138 35455 98.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 115.81 Å2 / Biso mean: 55.801 Å2 / Biso min: 23.68 Å2
Baniso -1Baniso -2Baniso -3
1-1.28 Å20 Å2-0.64 Å2
2---0.66 Å20 Å2
3----0.96 Å2
Refinement stepCycle: final / Resolution: 2.15→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4473 0 0 109 4582
Biso mean---42.27 -
Num. residues----561
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0224570
X-RAY DIFFRACTIONr_angle_refined_deg1.9691.9476170
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0465559
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.99725.024211
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.84215841
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1221516
X-RAY DIFFRACTIONr_chiral_restr0.1410.2689
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0213397
X-RAY DIFFRACTIONr_mcbond_it1.0661.52801
X-RAY DIFFRACTIONr_mcangle_it1.97524526
X-RAY DIFFRACTIONr_scbond_it3.23931769
X-RAY DIFFRACTIONr_scangle_it4.8954.51643
LS refinement shellResolution: 2.15→2.199 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.355 141 -
Rwork0.267 2540 -
all-2681 -
obs--96.89 %
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)
10.21910.0510.76420.03940.28134.0185-0.08970.0488-0.02530.00660.0514-0.02880.07360.07250.03820.1726-0.07490.01970.1461-0.05670.1153-0.3110.239713.4473
20.4098-0.1436-0.43432.98312.18212.91240.0067-0.1273-0.10640.1470.0513-0.29360.31090.1097-0.0580.0547-0.0079-0.0230.06640.02650.1425-20.8586-16.409340.8077
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A30 - 317
2X-RAY DIFFRACTION2B30 - 317

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