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- PDB-4dxf: Crystal structure of Staphylococcal Superantigen-Like protein 4 -

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Basic information

Entry
Database: PDB / ID: 4dxf
TitleCrystal structure of Staphylococcal Superantigen-Like protein 4
ComponentsStaphylococcal enterotoxin-like toxin
KeywordsSUGAR BINDING PROTEIN / Oligonucleotide/oligosaccharide binding fold / beta grasp fold / Superantigen fold / Carbohydrate binding
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
Staphylococcal superantigen-like 4 / Staphylococcal superantigen-like 4
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsHermans, S.J. / Baker, H.M. / Langley, R.J. / Baker, E.N. / Fraser, J.F.
CitationJournal: Infect.Immun. / Year: 2012
Title: Structural and functional properties of staphylococcal superantigen-like protein 4
Authors: Hermans, S.J. / Baker, H.M. / Sequeira, R.P. / Langley, R.J. / Baker, E.N. / Fraser, J.D.
History
DepositionFeb 27, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 19, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 12, 2014Group: Database references
Revision 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Staphylococcal enterotoxin-like toxin
B: Staphylococcal enterotoxin-like toxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,0327
Polymers46,7982
Non-polymers2345
Water5,693316
1
A: Staphylococcal enterotoxin-like toxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,4342
Polymers23,3991
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Staphylococcal enterotoxin-like toxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,5975
Polymers23,3991
Non-polymers1984
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)96.102, 81.195, 57.301
Angle α, β, γ (deg.)90.00, 105.45, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Staphylococcal enterotoxin-like toxin / Superantigen-Like protein 4


Mass: 23398.969 Da / Num. of mol.: 2 / Fragment: UNP residues 109-308
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: Newman / Gene: NWMN_0391, ssl4nm / Plasmid: pET-32a.3c / Production host: Escherichia coli (E. coli) / Strain (production host): AD494 / References: UniProt: A6QE81, UniProt: A0A0H3K6A3*PLUS
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 316 / 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: 2.3 Å3/Da / Density % sol: 46.57 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 21% MPEG 5000, 0.2M bis-tris propane, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: May 5, 2010 / Details: Osmic mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.7→27.62 Å / Num. obs: 46435 / % possible obs: 99.7 % / Redundancy: 9.9 % / Biso Wilson estimate: 28.8 Å2 / Rmerge(I) obs: 0.058 / Net I/σ(I): 17.14
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allDiffraction-ID% possible all
1.7-1.789.60.6986696199.2
1.79-1.899.70.3896390199.5
1.9-2.029.80.2416033199.8
2.03-2.189.90.15355921100
2.19-2.39100.10951881100
2.4-2.6810.10.07646791100
2.69-3.0910.20.05641481100
3.1-3.7910.30.04435231100
3.8-5.3710.30.0372718199.8
5.38-27.62100.0391468196.4

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
REFMAC5.5.0109refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 2RDH and 2Z8L

2rdh

2z8l


Resolution: 1.7→27.62 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.936 / SU B: 3.085 / SU ML: 0.099 / Cross valid method: THROUGHOUT / ESU R: 0.122 / ESU R Free: 0.127 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2614 2345 5.1 %RANDOM
Rwork0.20864 ---
obs0.21126 44078 99.55 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.686 Å2
Baniso -1Baniso -2Baniso -3
1--1.98 Å20 Å2-1.72 Å2
2--0.91 Å2-0 Å2
3---0.16 Å2
Refinement stepCycle: LAST / Resolution: 1.7→27.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3108 0 10 316 3434
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.0223175
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.0961.9644258
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.95386
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.41225.541148
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.34815643
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.4081511
X-RAY DIFFRACTIONr_chiral_restr0.1570.2471
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022315
X-RAY DIFFRACTIONr_gen_planes_other
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_it1.4071.51903
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.35323087
X-RAY DIFFRACTIONr_scbond_it3.42331272
X-RAY DIFFRACTIONr_scangle_it5.5544.51169
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.554 175 -
Rwork0.525 3196 -
obs--98.91 %

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