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- PDB-1i4h: Crystal structure of Zn2+ soaked Staphylococcal enterotoxin A mut... -

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Basic information

Entry
Database: PDB / ID: 1i4h
TitleCrystal structure of Zn2+ soaked Staphylococcal enterotoxin A mutant H187A
ComponentsENTEROTOXIN TYPE A
KeywordsTOXIN / beta-grasp / beta-barrel
Function / homology
Function and homology information


MHC class II protein binding / toxin activity / extracellular region / metal ion binding
Similarity search - Function
Staphylococcal enterotoxin/Streptococcal pyrogenic exotoxin signature 1. / 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 ...Staphylococcal enterotoxin/Streptococcal pyrogenic exotoxin signature 1. / 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 / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsHakansson, M. / Antonsson, P. / Bjork, P. / Svensson, L.A.
CitationJournal: J.Biol.Inorg.Chem. / Year: 2001
Title: Cooperative zinc binding in a staphylococcal enterotoxin A mutant mimics the SEA-MHC class II interaction
Authors: Hakansson, M. / Antonsson, P. / Bjork, P. / Svensson, L.A.
History
DepositionFeb 21, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 28, 2001Provider: 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: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Oct 27, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_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_conn.ptnr2_symmetry / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Aug 9, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.6Nov 6, 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 TYPE A
B: ENTEROTOXIN TYPE A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,2574
Polymers54,1262
Non-polymers1312
Water00
1
A: ENTEROTOXIN TYPE A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,1292
Polymers27,0631
Non-polymers651
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: ENTEROTOXIN TYPE A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,1292
Polymers27,0631
Non-polymers651
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)74.110, 85.060, 86.540
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein ENTEROTOXIN TYPE A / SEA


Mass: 27063.236 Da / Num. of mol.: 2 / Mutation: H187A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Plasmid: PKP889 / Production host: Escherichia coli (E. coli) / Strain (production host): UL635 / References: UniProt: P0A0L2
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
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: 2.52 Å3/Da / Density % sol: 46 %
Crystal growTemperature: 298 K / Method: evaporation / pH: 6
Details: PEG 8000, lithium sulphate, pipes, zinc chloride, pH 6.0, EVAPORATION, temperature 298K
Crystal grow
*PLUS
pH: 8 / Method: vapor diffusion
Details: drop was mixed with an equal volume of reservoir solution
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlprotein1drop
220 mMtricine1drop
315 %(w/v)PEG80001reservoir
4200 mM1reservoirLiSO4
5100 mMPIPES1reservoir

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 19, 1996
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.9→20 Å / Num. all: 10658 / Num. obs: 10658 / % possible obs: 84.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Biso Wilson estimate: 58.9 Å2 / Rmerge(I) obs: 0.087 / Net I/σ(I): 13.2
Reflection shellResolution: 2.9→3 Å / Redundancy: 4 % / Rmerge(I) obs: 0.269 / Mean I/σ(I) obs: 3.2 / Num. unique all: 1039 / % possible all: 88.1
Reflection
*PLUS
Num. measured all: 43647
Reflection shell
*PLUS
% possible obs: 88.1 %

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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: pdb entry 1I4G

1i4g


Resolution: 2.9→20 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.281 450 random
Rwork0.208 --
all-10658 -
obs-10658 -
Displacement parametersBiso mean: 40.9 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.51 Å0.33 Å
Luzzati d res low-5 Å
Luzzati sigma a0.6 Å0.42 Å
Refinement stepCycle: LAST / Resolution: 2.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3689 0 2 0 3691
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_d1.31
X-RAY DIFFRACTIONc_dihedral_angle_d24.9
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_deg1.31
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.9

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