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- PDB-1dyq: STAPHYLOCOCCAL ENTEROTOXIN A MUTANT VACCINE -

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Basic information

Entry
Database: PDB / ID: 1dyq
TitleSTAPHYLOCOCCAL ENTEROTOXIN A MUTANT VACCINE
ComponentsEnterotoxin type A
KeywordsENTEROTOXIN / STAPHYLOCOCCAL ENTEROTOXIN TYPE A / VACCINE
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsKrupka, H.I. / Segelke, B.W. / Rupp, B.
CitationJournal: Protein Sci. / Year: 2002
Title: Structural Basis for Abrogated Binding between Staphylococcal Enterotoxin a Superantigen Vaccine and Mhc-II?
Authors: Krupka, H.I. / Segelke, B.W. / Ulrich, R. / Ringhofer, S. / Knapp, M. / Rupp, B.
History
DepositionFeb 5, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 19, 2001Provider: repository / Type: Initial release
Revision 1.1May 7, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 3, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval
Revision 1.4May 8, 2019Group: Data collection / Experimental preparation
Category: database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow
Item: _exptl_crystal_grow.method
Revision 1.5Sep 25, 2019Group: Advisory / Data collection ...Advisory / Data collection / Database references / Source and taxonomy / Structure summary
Category: entity / entity_src_gen ...entity / entity_src_gen / pdbx_poly_seq_scheme / pdbx_unobs_or_zero_occ_residues / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity.pdbx_description / _entity_src_gen.gene_src_strain ..._entity.pdbx_description / _entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_gene_src_scientific_name / _entity_src_gen.pdbx_seq_type / _pdbx_poly_seq_scheme.pdb_seq_num / _pdbx_unobs_or_zero_occ_residues.auth_seq_id
Revision 1.6Dec 6, 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_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.ptnr1_symmetry / _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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.7Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Remark 700 SHEET DETERMINATION METHOD: THERE IS A BIFURCATED SHEET IN THIS STRUCTURE. THIS SHEET REPRESENTED ... SHEET DETERMINATION METHOD: THERE IS A BIFURCATED SHEET IN THIS STRUCTURE. THIS SHEET REPRESENTED BY TWO SHEETS WHICH HAS TWO IDENTICAL STRANDS. SHEETS A AND A1 REPRESENT ONE BIFURCATED SHEET.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Enterotoxin type A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,4173
Polymers27,2561
Non-polymers1612
Water8,899494
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)39.048, 78.652, 86.374
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsBIOLOGICAL UNIT: MONOMER

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Components

#1: Protein Enterotoxin type A / SEA


Mass: 27255.547 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Description: MUTANT GENE / Gene: entA / Plasmid: PSE380 / Gene (production host): FDA196E / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): JM101 / References: UniProt: P0A0L2
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 494 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsVACCINE MUTANT L48R, Y92A, D70R

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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: 2.5 Å3/Da / Density % sol: 51 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: HANGING DROP OVER 1 ML WELL, 4 + 4 UL DROPS, WELL SOLUTION 10% PEG6K, 5% MPD IN 0.1 M HEPES PH 7.8, TEMPERATURE 4 DEG, 3-4 WEEKS.
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, hanging drop / pH: 7.8
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 %PEG60001reservoir
25 %MPD1reservoir
30.1 MHEPES1reservoirpH7.8
42 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1.1
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 15, 1999 / Details: DOUBLE FOCUSSING
RadiationMonochromator: SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.5→43.19 Å / Num. obs: 35972 / % possible obs: 82.8 % / Redundancy: 4.5 % / Biso Wilson estimate: 17.5 Å2 / Rsym value: 0.061 / Net I/σ(I): 7
Reflection shellResolution: 1.5→1.54 Å / Redundancy: 2.8 % / Mean I/σ(I) obs: 4.4 / Rsym value: 0.135 / % possible all: 46.7
Reflection
*PLUS
Num. measured all: 158285 / Rmerge(I) obs: 0.062
Reflection shell
*PLUS
% possible obs: 37.2 % / Num. unique obs: 1143 / Num. measured obs: 2752 / Rmerge(I) obs: 0.135 / Mean I/σ(I) obs: 3.4

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Processing

Software
NameClassification
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
EPMRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ESF

1esf


Resolution: 1.5→43.187 Å / SU B: 1.726 / SU ML: 0.063 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.097 / ESU R Free: 0.101
Details: RESIDUES GLU 9, ASP 60 AND GLU 191 ARE IN WEAK DENSITY AND SIDE CHAIN ATOMS WERE NOT REFINED.
RfactorNum. reflection% reflectionSelection details
Rfree0.236 1830 5 %RANDOM
Rwork0.191 ---
obs-35972 82.84 %-
Displacement parametersBiso mean: 20 Å2
Refinement stepCycle: LAST / Resolution: 1.5→43.187 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1861 0 6 494 2361
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0160.02
X-RAY DIFFRACTIONp_angle_d0.0180.02
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0260.03
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.562
X-RAY DIFFRACTIONp_mcangle_it2.2683
X-RAY DIFFRACTIONp_scbond_it2.7713
X-RAY DIFFRACTIONp_scangle_it3.9024
X-RAY DIFFRACTIONp_plane_restr0.0260.03
X-RAY DIFFRACTIONp_chiral_restr0.1510.15
X-RAY DIFFRACTIONp_singtor_nbd0.1810.3
X-RAY DIFFRACTIONp_multtor_nbd0.2640.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.0930.3
X-RAY DIFFRACTIONp_planar_tor5.0867
X-RAY DIFFRACTIONp_staggered_tor14.52915
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor27.01520
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.191
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg2.069

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