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- PDB-5lq7: Salmonella effector SpvD - G161 variant -

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Basic information

Entry
Database: PDB / ID: 5lq7
TitleSalmonella effector SpvD - G161 variant
ComponentsVirulence protein vsdE
KeywordsIMMUNOSUPPRESSANT / Effector / signaling protein
Function / homologySalmonella plasmid virulence SpvD / Salmonella plasmid virulence protein SpvD / DI(HYDROXYETHYL)ETHER / Virulence protein vsdE
Function and homology information
Biological speciesSalmonella enterica (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsPrzydacz, M. / Grabe, G.J. / Holden, D.W. / Hare, S.A.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)G1100332/1 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 2.0Sep 13, 2017Group: Atomic model / Author supporting evidence / Category: atom_site / pdbx_audit_support
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _pdbx_audit_support.funding_organization
Revision 2.1Jan 10, 2024Group: 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

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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)25,2036
Polymers24,8941
Non-polymers3105
Water3,693205
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1010 Å2
ΔGint-20 kcal/mol
Surface area11060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.000, 51.970, 47.220
Angle α, β, γ (deg.)90.00, 107.70, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Virulence protein vsdE


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 / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 205 / 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: 2.07 Å3/Da / Density % sol: 40.47 %
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: I02 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 12, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 1.6→1.69 Å / Redundancy: 6 % / Mean I/σ(I) obs: 1.9 / CC1/2: 0.579 / % possible all: 99.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0107refinement
iMOSFLMdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5LQ6

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
RfactorNum. reflection% reflectionSelection details
Rfree0.1973 1333 5 %RANDOM
Rwork0.16319 ---
obs0.1649 25387 99.23 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 20.415 Å2
Baniso -1Baniso -2Baniso -3
1-0.21 Å20 Å2-0.73 Å2
2---0.24 Å20 Å2
3---0.41 Å2
Refinement stepCycle: 1 / Resolution: 1.6→44.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1664 0 18 205 1887
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0191768
X-RAY DIFFRACTIONr_bond_other_d0.0060.021691
X-RAY DIFFRACTIONr_angle_refined_deg1.411.952407
X-RAY DIFFRACTIONr_angle_other_deg0.98733906
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8355226
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.5125.11190
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.56315322
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.048159
X-RAY DIFFRACTIONr_chiral_restr0.1040.2272
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022026
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02413
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_it2.2251.667846
X-RAY DIFFRACTIONr_mcbond_other2.2241.663844
X-RAY DIFFRACTIONr_mcangle_it3.2562.4831060
X-RAY DIFFRACTIONr_mcangle_other3.2552.4881061
X-RAY DIFFRACTIONr_scbond_it4.0262.164922
X-RAY DIFFRACTIONr_scbond_other4.0212.163922
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.23.0351337
X-RAY DIFFRACTIONr_long_range_B_refined7.7615.2042213
X-RAY DIFFRACTIONr_long_range_B_other7.75815.2182214
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.6→1.641 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.262 99 -
Rwork0.262 1862 -
obs--98.89 %

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