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- PDB-1ewc: CRYSTAL STRUCTURE OF ZN2+ LOADED STAPHYLOCOCCAL ENTEROTOXIN H -

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Basic information

Entry
Database: PDB / ID: 1ewc
TitleCRYSTAL STRUCTURE OF ZN2+ LOADED STAPHYLOCOCCAL ENTEROTOXIN H
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. / Superantigen, staphylococcal/streptococcal toxin, bacterial / Staphylococcal/Streptococcal toxin, beta-grasp domain / Staphylococcal/Streptococcal toxin, beta-grasp domain / 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 enterotoxin/Streptococcal pyrogenic exotoxin, conserved site / Staphyloccocal enterotoxin/Streptococcal pyrogenic exotoxin signature 2. / Superantigen, staphylococcal/streptococcal toxin, bacterial / Staphylococcal/Streptococcal toxin, beta-grasp domain / Staphylococcal/Streptococcal toxin, beta-grasp domain / 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: 1.95 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
DepositionApr 25, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 31, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model
Revision 1.4Oct 4, 2017Group: Data collection / Refinement description / Category: diffrn_source / software
Item: _diffrn_source.pdbx_synchrotron_site / _software.classification / _software.name
Revision 1.5Aug 9, 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_conn / 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_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.6Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)24,8162
Polymers24,7511
Non-polymers651
Water2,702150
1


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

A: ENTEROTOXIN H
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,6324
Polymers49,5012
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation16_545y+1/3,x-1/3,-z+2/31
Buried area1360 Å2
ΔGint-85 kcal/mol
Surface area18830 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)74,4486
Polymers74,2523
Non-polymers1963
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)86.380, 86.380, 228.790
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-381-

HOH

21A-386-

HOH

31A-389-

HOH

41A-415-

HOH

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Components

#1: Protein ENTEROTOXIN H


Mass: 24750.686 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-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 150 / 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: 3.32 Å3/Da / Density % sol: 62.93 %
Crystal growTemperature: 298 K / Method: evaporation / pH: 4.6
Details: 20% iso-propanol, 100 mM sodium acetate pH 4.6, 200 mM CaCl2, 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
220 %(v/v)isopropanol1reservoir
3100 mMsodium acetate1reservoir
4200 mM1reservoirCaCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 0.99
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: May 6, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99 Å / Relative weight: 1
ReflectionResolution: 1.95→22 Å / Num. all: 24645 / Num. obs: 22772 / % possible obs: 92.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.6 % / Biso Wilson estimate: 18.1 Å2 / Rsym value: 0.082
Reflection shellResolution: 1.95→2 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 3.1 / Num. unique all: 1665 / Rsym value: 0.246 / % possible all: 94.9
Reflection
*PLUS
Rmerge(I) obs: 0.082
Reflection shell
*PLUS
% possible obs: 94.9 % / Rmerge(I) obs: 0.246

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Processing

Software
NameVersionClassification
XDSdata scaling
TRUNCATEdata reduction
CNSrefinement
XDSdata reduction
CCP4(TRUNCATE)data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ENF

1enf


Resolution: 1.95→22 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 2507820.72 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.252 1144 5.1 %RANDOM
Rwork0.23 ---
obs0.227 22772 92.4 %-
all-24645 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 51.49 Å2 / ksol: 0.371 e/Å3
Displacement parametersBiso mean: 37.2 Å2
Baniso -1Baniso -2Baniso -3
1-6.39 Å23.31 Å20 Å2
2--6.39 Å20 Å2
3----12.79 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.32 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.41 Å0.34 Å
Refinement stepCycle: LAST / Resolution: 1.95→22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1731 0 1 150 1882
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.51
X-RAY DIFFRACTIONc_dihedral_angle_d25.7
X-RAY DIFFRACTIONc_improper_angle_d0.78
X-RAY DIFFRACTIONc_mcbond_it1.2941.5
X-RAY DIFFRACTIONc_mcangle_it1.982
X-RAY DIFFRACTIONc_scbond_it2.0672
X-RAY DIFFRACTIONc_scangle_it3.0582.5
LS refinement shellResolution: 1.95→2.07 Å / Rfactor Rfree error: 0.026 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.368 200 5.1 %
Rwork0.325 3687 -
obs--96.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ION.PARAMWATER.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMION.TOP
Software
*PLUS
Name: CNS / Version: 0.9 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 22 Å / σ(F): 0 / % reflection Rfree: 5.1 % / Rfactor obs: 0.23 / Rfactor Rwork: 0.23
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 37.2 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg25.7
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.78
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: 0.368 / % reflection Rfree: 5.1 % / Rfactor Rwork: 0.325

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