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- PDB-1f77: STAPHYLOCOCCAL ENTEROTOXIN H DETERMINED TO 2.4 A RESOLUTION -

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Basic information

Entry
Database: PDB / ID: 1f77
TitleSTAPHYLOCOCCAL ENTEROTOXIN H DETERMINED TO 2.4 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 enterotoxin/Streptococcal pyrogenic exotoxin, conserved site / Staphyloccocal enterotoxin/Streptococcal pyrogenic exotoxin signature 2. / Ubiquitin-like (UB roll) - #120 / Superantigen, staphylococcal/streptococcal toxin, bacterial / Staphylococcal/Streptococcal toxin, beta-grasp domain / Staphylococcal/Streptococcal toxin, beta-grasp domain / Superantigen toxin, C-terminal ...Staphylococcal/streptococcal toxin, bacterial / Staphylococcal/Streptococcal toxin, OB-fold / Staphylococcal/Streptococcal toxin, OB-fold domain / Staphylococcal enterotoxin/Streptococcal pyrogenic exotoxin, conserved site / Staphyloccocal enterotoxin/Streptococcal pyrogenic exotoxin signature 2. / Ubiquitin-like (UB roll) - #120 / Superantigen, staphylococcal/streptococcal toxin, bacterial / Staphylococcal/Streptococcal toxin, beta-grasp domain / Staphylococcal/Streptococcal toxin, beta-grasp domain / 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 / Resolution: 2.4 Å
AuthorsHakansson, M. / Petersson, K. / Nilsson, H. / Forsberg, G. / Bjork, P.
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
DepositionJun 26, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 19, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Data collection / Refinement description / Category: diffrn_source / software
Item: _diffrn_source.pdbx_synchrotron_site / _software.classification / _software.name
Revision 1.4Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: ENTEROTOXIN H
B: ENTEROTOXIN H
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,0339
Polymers50,3602
Non-polymers6727
Water3,441191
1
A: ENTEROTOXIN H
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,3723
Polymers25,1801
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: ENTEROTOXIN H
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,6616
Polymers25,1801
Non-polymers4805
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.26, 103.39, 117.14
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein ENTEROTOXIN H


Mass: 25180.240 Da / Num. of mol.: 2
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


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 191 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.9 Å3/Da / Density % sol: 57.6 %
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, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.935 Å / Relative weight: 1
ReflectionResolution: 2.4→25 Å / Num. all: 79561 / Num. obs: 23703 / % possible obs: 95 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 34.9 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 14.8
Reflection shellResolution: 2.4→2.5 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.326 / Num. unique all: 2583 / % possible all: 97
Reflection
*PLUS
Highest resolution: 2.4 Å / % possible obs: 95.8 % / Rmerge(I) obs: 0.08
Reflection shell
*PLUS
% possible obs: 97 %

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Processing

Software
NameVersionClassification
XDSdata scaling
TRUNCATEdata reduction
AMoREphasing
CNS0.9refinement
XDSdata reduction
CCP4(TRUNCATE)data scaling
RefinementResolution: 2.4→15 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: Used maximum likelihood function
RfactorNum. reflection% reflectionSelection details
Rfree0.253 1164 -random
Rwork0.214 ---
all-22568 --
obs--95.8 %-
Refinement stepCycle: LAST / Resolution: 2.4→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3433 0 35 191 3659
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_d25.2
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_bond_d0.008
Software
*PLUS
Name: CNS / Version: 0.9 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.4 Å / Lowest resolution: 15 Å / σ(F): 0 / Rfactor obs: 0.214
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: c_angle_d

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