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- PDB-5d3d: Crystal structure of Staphylococcal Superantigen-Like protein 3 -

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Basic information

Entry
Database: PDB / ID: 5d3d
TitleCrystal structure of Staphylococcal Superantigen-Like protein 3
ComponentsStaphylococcal Superantigen-Like protein 3
KeywordsIMMUNE SYSTEM / Superantigens / Superantigen-like proteins / SSL / SSL3 / Toll-Like Receptor 2 / TLR2 / Immunology / Inflammation / Inhibition
Function / homology
Function and homology information


extracellular region
Similarity search - Function
Staphylococcus aureus exotoxin / Staphylococcal superantigen-like OB-fold domain / Staphylococcal superantigen-like OB-fold domain / Staphylococcal enterotoxin/Streptococcal pyrogenic exotoxin, conserved site / Staphyloccocal enterotoxin/Streptococcal pyrogenic exotoxin signature 2. / Superantigen, staphylococcal/streptococcal toxin, bacterial / Ubiquitin-like (UB roll) - #120 / Superantigen toxin, C-terminal / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #110 / Enterotoxin ...Staphylococcus aureus exotoxin / Staphylococcal superantigen-like OB-fold domain / Staphylococcal superantigen-like OB-fold domain / Staphylococcal enterotoxin/Streptococcal pyrogenic exotoxin, conserved site / Staphyloccocal enterotoxin/Streptococcal pyrogenic exotoxin signature 2. / Superantigen, staphylococcal/streptococcal toxin, bacterial / Ubiquitin-like (UB roll) - #120 / Superantigen toxin, C-terminal / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #110 / Enterotoxin / Ubiquitin-like (UB roll) / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Roll / Beta Barrel / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
THIOCYANATE ION / Staphylococcal superantigen-like 3
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.94 Å
AuthorsFeitsma, L.J. / Huizinga, E.G.
Funding support Netherlands, 3items
OrganizationGrant numberCountry
Netherlands Organization for Scientific ResearchECHO Grant 700.58.006 Netherlands
Netherlands Organization for Health Research and DevelopmentZonMw Grant 205200004 Netherlands
Dutch Top Institute Pharma ProjectD1-101 Netherlands
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2015
Title: Structural basis for inhibition of TLR2 by staphylococcal superantigen-like protein 3 (SSL3).
Authors: Koymans, K.J. / Feitsma, L.J. / Brondijk, T.H. / Aerts, P.C. / Lukkien, E. / Lossl, P. / van Kessel, K.P. / de Haas, C.J. / van Strijp, J.A. / Huizinga, E.G.
History
DepositionAug 6, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Aug 19, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 2, 2015Group: Database references
Revision 1.2Sep 9, 2015Group: Database references
Revision 1.3May 1, 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: Staphylococcal Superantigen-Like protein 3
B: Staphylococcal Superantigen-Like protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,43814
Polymers45,6972
Non-polymers74112
Water3,855214
1
A: Staphylococcal Superantigen-Like protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,2898
Polymers22,8491
Non-polymers4417
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Staphylococcal Superantigen-Like protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,1496
Polymers22,8491
Non-polymers3015
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.000, 79.220, 96.380
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Staphylococcal Superantigen-Like protein 3


Mass: 22848.506 Da / Num. of mol.: 2 / Fragment: UNP residues 164-356
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (strain NCTC 8325) (bacteria)
Gene: SAOUHSC_00386 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): Rosetta-gami / References: UniProt: Q2G0X7

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Non-polymers , 5 types, 226 molecules

#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-SCN / THIOCYANATE ION


Mass: 58.082 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CNS
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-NA / SODIUM ION


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


Mass: 18.015 Da / Num. of mol.: 214 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.46 Å3/Da / Density % sol: 50 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.2 / Details: PEG 3350, potassium thiocyanate

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9999 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Mar 30, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 1.94→61.2 Å / Num. obs: 33556 / % possible obs: 99.8 % / Redundancy: 6.7 % / Biso Wilson estimate: 32.2 Å2 / Rmerge(I) obs: 0.093 / Net I/σ(I): 11.1
Reflection shellResolution: 1.94→1.99 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.73 / Mean I/σ(I) obs: 2.7 / % possible all: 99.9

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Processing

Software
NameVersionClassification
MOSFLM1.0.6data reduction
Aimless1.7.6data scaling
PHASER2.5.2phasing
REFMAC5.8.0073refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: SSL4

Resolution: 1.94→61.2 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.934 / SU B: 7.832 / SU ML: 0.111 / Cross valid method: FREE R-VALUE / ESU R: 0.155 / ESU R Free: 0.147 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22431 1694 5.1 %RANDOM
Rwork0.17635 ---
obs0.17874 31805 99.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.308 Å2
Baniso -1Baniso -2Baniso -3
1-1.54 Å2-0 Å20 Å2
2---0.22 Å2-0 Å2
3----1.32 Å2
Refinement stepCycle: 1 / Resolution: 1.94→61.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3178 0 41 214 3433
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0193371
X-RAY DIFFRACTIONr_bond_other_d0.0010.023363
X-RAY DIFFRACTIONr_angle_refined_deg1.2061.9764520
X-RAY DIFFRACTIONr_angle_other_deg0.66837812
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9035416
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.49625.195154
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.47315710
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.5441512
X-RAY DIFFRACTIONr_chiral_restr0.0740.2491
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023682
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02734
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_it1.132.341577
X-RAY DIFFRACTIONr_mcbond_other1.132.341576
X-RAY DIFFRACTIONr_mcangle_it1.793.4981975
X-RAY DIFFRACTIONr_mcangle_other1.793.4981976
X-RAY DIFFRACTIONr_scbond_it1.4852.5971794
X-RAY DIFFRACTIONr_scbond_other1.4852.5971794
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.4293.7892530
X-RAY DIFFRACTIONr_long_range_B_refined5.23819.1383847
X-RAY DIFFRACTIONr_long_range_B_other5.08118.7863783
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.94→1.99 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.278 108 -
Rwork0.269 2307 -
obs--99.83 %
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)
11.48670.13060.37112.08221.15822.18120.03830.1332-0.213-0.15270.0631-0.04090.10760.0052-0.10140.09570.0236-0.02380.0395-0.01370.0545-9.5907-12.186413.3197
21.36520.56670.96951.63650.942.87160.001-0.0539-0.06630.05260.0003-0.09-0.155-0.0029-0.00130.06740.0154-0.00970.01570.01050.0202-4.01391.097527.9603
31.6661-0.39850.27082.395-0.17432.24550.0446-0.03-0.08120.01360.02020.05150.17410.1216-0.06480.067-0.01290.00780.02280.00070.027923.6522-4.04272.8254
41.8761-0.2928-0.40112.2687-0.29482.87680.124-0.14360.34240.21630.08510.0334-0.6781-0.0383-0.20910.2404-0.00690.0780.022-0.0210.102318.040614.32279.3442
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 223
2X-RAY DIFFRACTION2A224 - 326
3X-RAY DIFFRACTION3B1 - 223
4X-RAY DIFFRACTION4B224 - 326

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