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- PDB-6kry: Structure of staphylococcal enterotoxin SEN -

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Basic information

Entry
Database: PDB / ID: 6kry
TitleStructure of staphylococcal enterotoxin SEN
ComponentsEnterotoxin SEN variant
KeywordsALLERGEN / staphylococcal enterotoxin / SEN
Function / homology
Function and homology information


: / toxin activity / extracellular region
Similarity search - Function
Staphylococcal/streptococcal toxin, bacterial / Staphylococcal/Streptococcal toxin, OB-fold / Staphylococcal/Streptococcal toxin, OB-fold domain / Staphylococcal/Streptococcal toxin, beta-grasp domain / Staphylococcal/Streptococcal toxin, beta-grasp 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 ...Staphylococcal/streptococcal toxin, bacterial / Staphylococcal/Streptococcal toxin, OB-fold / Staphylococcal/Streptococcal toxin, OB-fold domain / Staphylococcal/Streptococcal toxin, beta-grasp domain / Staphylococcal/Streptococcal toxin, beta-grasp 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
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsHan, Z. / Zeng, C.
CitationJournal: Int J Mol Sci / Year: 2019
Title: Structure of Staphylococcal Enterotoxin N: Implications for Binding Properties to Its Cellular Proteins.
Authors: Zeng, C. / Liu, Z. / Han, Z.
History
DepositionAug 22, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 4, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 11, 2019Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.pdbx_database_id_PubMed
Revision 1.2May 13, 2020Group: Structure summary / Category: struct / Item: _struct.title
Revision 1.3Mar 27, 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: Enterotoxin SEN variant


Theoretical massNumber of molelcules
Total (without water)26,1451
Polymers26,1451
Non-polymers00
Water3,081171
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.000, 64.420, 50.140
Angle α, β, γ (deg.)90.000, 110.030, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Enterotoxin SEN variant / Enterotoxin SeN


Mass: 26145.215 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: sen, ERS072840_00070, NCTC7878_02454 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6YCN3
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 171 / 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: 2.47 Å3/Da / Density % sol: 50.17 %
Crystal growTemperature: 277 K / Method: evaporation / pH: 8
Details: 10 mM Tris pH 8.0, 2% (v/v) Tacsimate TM pH 4.0, 0.1 M Sodium acetate trihydrate pH 4.6, 16% (W/v) polyethylene glycol 3350.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 22, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 1.8→64.42 Å / Num. obs: 23007 / % possible obs: 98.5 % / Redundancy: 6 % / Biso Wilson estimate: 11.5 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.113 / Net I/σ(I): 11.4
Reflection shellResolution: 1.8→1.9 Å / Rmerge(I) obs: 0.58 / Num. unique obs: 3343 / CC1/2: 0.859

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Processing

Software
NameVersionClassification
REFMAC5.8.0222refinement
PDB_EXTRACT3.25data extraction
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→47.11 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.935 / SU B: 2.793 / SU ML: 0.085 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.119 / ESU R Free: 0.115
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2075 1151 5 %RANDOM
Rwork0.1706 ---
obs0.1724 21836 98.38 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 68.61 Å2 / Biso mean: 18.872 Å2 / Biso min: 7.99 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å2-0 Å2-0 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 1.8→47.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1821 0 0 171 1992
Biso mean---27.67 -
Num. residues----224
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0141853
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171663
X-RAY DIFFRACTIONr_angle_refined_deg1.5411.6472495
X-RAY DIFFRACTIONr_angle_other_deg0.9941.6563896
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5865223
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.88325.5198
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.14615346
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.857153
X-RAY DIFFRACTIONr_chiral_restr0.070.2242
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022061
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02363
LS refinement shellResolution: 1.8→1.847 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.285 80 -
Rwork0.24 1578 -
all-1658 -
obs--97.3 %

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