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- PDB-1enf: CRYSTAL STRUCTURE OF STAPHYLOCOCCAL ENTEROTOXIN H DETERMINED TO 1... -

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Basic information

Entry
Database: PDB / ID: 1enf
TitleCRYSTAL STRUCTURE OF STAPHYLOCOCCAL ENTEROTOXIN H DETERMINED TO 1.69 A RESOLUTION
ComponentsENTEROTOXIN H
KeywordsTOXIN / beta-barrel / beta-grasp
Function / homology
Function and homology information


MHC class II protein binding / T cell receptor binding / toxin activity / extracellular region / metal ion binding
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: 1.69 Å
AuthorsHakansson, M. / Petersson, K. / Nilsson, H. / Forsberg, G. / Bjork, P. / Antonsson, P. / Svensson, A.
CitationJournal: J.Mol.Biol. / Year: 2000
Title: The crystal structure of staphylococcal enterotoxin H: implications for binding properties to MHC class II and TcR molecules.
Authors: Hakansson, M. / Petersson, K. / Nilsson, H. / Forsberg, G. / Bjork, P. / Antonsson, P. / Svensson, L.A.
History
DepositionMar 21, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 19, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 4, 2017Group: Data collection / Refinement description / Category: diffrn_source / software / Item: _diffrn_source.pdbx_synchrotron_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ENTEROTOXIN H
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,81314
Polymers24,5641
Non-polymers1,24913
Water4,432246
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: ENTEROTOXIN H
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)154,88084
Polymers147,3876
Non-polymers7,49378
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_765-y+2,x-y+1,z1
crystal symmetry operation3_675-x+y+1,-x+2,z1
crystal symmetry operation4_556y,x,-z+11
crystal symmetry operation5_676x-y+1,-y+2,-z+11
crystal symmetry operation6_766-x+2,-x+y+1,-z+11
Buried area27380 Å2
ΔGint-1134 kcal/mol
Surface area46830 Å2
MethodPISA
3
A: ENTEROTOXIN H
hetero molecules

A: ENTEROTOXIN H
hetero molecules

A: ENTEROTOXIN H
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,44042
Polymers73,6933
Non-polymers3,74639
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_765-y+2,x-y+1,z1
crystal symmetry operation3_675-x+y+1,-x+2,z1
MethodPQS
Unit cell
Length a, b, c (Å)84.850, 84.850, 223.590
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-1009-

SO4

21A-1009-

SO4

31A-387-

HOH

41A-417-

HOH

51A-467-

HOH

61A-506-

HOH

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Components

#1: Protein ENTEROTOXIN H


Mass: 24564.455 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Plasmid: PLR16 / Production host: Escherichia coli (E. coli) / Strain (production host): UL635 / References: UniProt: P0A0M0
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 246 / 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: 3.15 Å3/Da / Density % sol: 60.98 %
Crystal growTemperature: 298 K / Method: evaporation / pH: 4.3
Details: 16% PEG 8000, 500 mM Li2SO4, 5 mM CaCl2, pH 4.3, EVAPORATION, temperature 298K
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlprotein1drop
216 %(w/v)PEG80001reservoir
3500 mM1reservoirLi2SO4
45 mM1reservoirCaCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 0.935
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 18, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.935 Å / Relative weight: 1
ReflectionResolution: 1.69→23 Å / Num. all: 35745 / Num. obs: 33815 / % possible obs: 95 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Biso Wilson estimate: 16.8 Å2 / Rmerge(I) obs: 0.052
Reflection shellResolution: 1.68→1.75 Å / Rmerge(I) obs: 0.225 / % possible all: 71
Reflection shell
*PLUS
% possible obs: 71 %

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Processing

Software
NameVersionClassification
MAR345data collection
XDSdata reduction
AMoREphasing
CNS0.5refinement
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.69→23 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 2486052.54 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.187 1686 5 %RANDOM
Rwork0.164 ---
obs0.164 33813 96.1 %-
all-33815 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 49.99 Å2 / ksol: 0.438 e/Å3
Displacement parametersBiso mean: 18.1 Å2
Baniso -1Baniso -2Baniso -3
1-1.93 Å21.84 Å20 Å2
2--1.93 Å20 Å2
3----3.87 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.17 Å0.15 Å
Luzzati d res low-5 Å
Luzzati sigma a0.09 Å0.08 Å
Refinement stepCycle: LAST / Resolution: 1.69→23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1726 0 65 246 2037
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.023
X-RAY DIFFRACTIONc_angle_deg2
X-RAY DIFFRACTIONc_dihedral_angle_d26.2
X-RAY DIFFRACTIONc_improper_angle_d1.37
X-RAY DIFFRACTIONc_mcbond_it1.011.5
X-RAY DIFFRACTIONc_mcangle_it1.492
X-RAY DIFFRACTIONc_scbond_it2.052
X-RAY DIFFRACTIONc_scangle_it3.042.5
LS refinement shellResolution: 1.69→1.79 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.222 237 4.7 %
Rwork0.19 4827 -
obs--87.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER_REP.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
Software
*PLUS
Name: CNS / Version: 0.5 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 18.1 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg2
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg26.2
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.37
X-RAY DIFFRACTIONc_mcbond_it1.5
X-RAY DIFFRACTIONc_scbond_it2
X-RAY DIFFRACTIONc_mcangle_it2
X-RAY DIFFRACTIONc_scangle_it2.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.222 / % reflection Rfree: 4.7 % / Rfactor Rwork: 0.19

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