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- PDB-5lq6: Salmonella effector SpvD - R161 variant -

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Basic information

Entry
Database: PDB / ID: 5lq6
TitleSalmonella effector SpvD - R161 variant
ComponentsVirulence protein vsdE
KeywordsIMMUNOSUPPRESSANT / Effector / signaling protein
Function / homologySalmonella plasmid virulence SpvD / Salmonella plasmid virulence protein SpvD / Virulence protein vsdE
Function and homology information
Biological speciesSalmonella enterica (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.48 Å
AuthorsZhang, Y. / Grabe, G.J. / Rolhion, N. / Yang, Y. / Holden, D.W. / Hare, S.A.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom) United Kingdom
CitationJournal: 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
DepositionAug 16, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 2, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 9, 2016Group: Database references
Revision 1.2Dec 21, 2016Group: Database references
Revision 1.3Sep 13, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4May 8, 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: Virulence protein vsdE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,0492
Polymers25,0261
Non-polymers231
Water3,279182
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area150 Å2
ΔGint-11 kcal/mol
Surface area9970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.700, 51.810, 47.270
Angle α, β, γ (deg.)90.00, 107.41, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Virulence protein vsdE


Mass: 25025.941 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
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 182 / 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: 2.04 Å3/Da / Density % sol: 39.71 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 100 mM Tris, 200 mM NaCl, 22 % PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 21, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.48→51.81 Å / Num. obs: 33404 / % possible obs: 99.1 % / Redundancy: 5.9 % / Rmerge(I) obs: 0.076 / Net I/σ(I): 12.1
Reflection shellResolution: 1.48→1.56 Å / Redundancy: 4.6 % / Mean I/σ(I) obs: 2.1 / CC1/2: 0.532 / % possible all: 94.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0107refinement
iMOSFLMdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: SIRAS / Resolution: 1.48→45.1 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.95 / SU B: 1.337 / SU ML: 0.05 / Cross valid method: THROUGHOUT / ESU R: 0.068 / ESU R Free: 0.071 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20132 1736 5.2 %RANDOM
Rwork0.16957 ---
obs0.17114 31637 99.07 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 22.392 Å2
Baniso -1Baniso -2Baniso -3
1--0.22 Å20 Å2-0.72 Å2
2--0.4 Å20 Å2
3---0.23 Å2
Refinement stepCycle: 1 / Resolution: 1.48→45.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1503 0 1 182 1686
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0191593
X-RAY DIFFRACTIONr_bond_other_d0.0060.021526
X-RAY DIFFRACTIONr_angle_refined_deg1.5781.9462168
X-RAY DIFFRACTIONr_angle_other_deg1.0133523
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9675202
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.69925.17685
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.14215299
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.759159
X-RAY DIFFRACTIONr_chiral_restr0.1070.2244
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021830
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02379
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.1491.898756
X-RAY DIFFRACTIONr_mcbond_other2.141.896755
X-RAY DIFFRACTIONr_mcangle_it3.1852.824944
X-RAY DIFFRACTIONr_mcangle_other3.1842.827945
X-RAY DIFFRACTIONr_scbond_it3.5982.335837
X-RAY DIFFRACTIONr_scbond_other3.5842.327835
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.6913.3131212
X-RAY DIFFRACTIONr_long_range_B_refined7.7116.9861994
X-RAY DIFFRACTIONr_long_range_B_other7.66316.3721908
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.48→1.518 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.261 116 -
Rwork0.273 2091 -
obs--88.71 %

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