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- PDB-1uup: Crystal Structure of A Dimeric Form of Streptococcal Pyrogenic Ex... -

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Basic information

Entry
Database: PDB / ID: 1uup
TitleCrystal Structure of A Dimeric Form of Streptococcal Pyrogenic Exotoxin A (SpeA1).
ComponentsEXOTOXIN TYPE A
KeywordsTOXIN / MOLECULAR RECOGNITION / SUPERANTIGEN / EXOTOXIN / ZINC BINDING / DIMER
Function / homology
Function and homology information


toxin activity / extracellular region
Similarity search - Function
Staphylococcal enterotoxin/Streptococcal pyrogenic exotoxin signature 1. / 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 enterotoxin/Streptococcal pyrogenic exotoxin signature 1. / 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
Exotoxin type A / Exotoxin type A
Similarity search - Component
Biological speciesSTREPTOCOCCUS PYOGENES (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsBaker, M.D. / Gendlina, I. / Collins, C.M. / Acharya, K.R.
Citation
Journal: Protein Sci. / Year: 2004
Title: Crystal Structure of a Dimeric Form of Streptococcal Pyrogenic Exotoxin a (Spea1)
Authors: Baker, M.D. / Gendlina, I. / Collins, C.M. / Acharya, K.R.
#1: Journal: Embo J. / Year: 1999
Title: Structural Basis for the Recognition of Superantigen Steptococcal Pyrogenic Exotoxin A1 (Spea1) by Mhc Classii Molecules and T-Cell Receptors
Authors: Papageorgiou, A.C. / Collins, C.M. / Gutman, D.M. / Kline, J.B. / O'Brian, S.M. / Tranter, H.S. / Acharya, K.R.
History
DepositionJan 8, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 12, 2004Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 24, 2018Group: Data collection / Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain
Revision 1.4Dec 13, 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 / pdbx_struct_conn_angle / struct_conn
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.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.value / _struct_conn.pdbx_dist_value / _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
Revision 1.5Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: EXOTOXIN TYPE A
B: EXOTOXIN TYPE A
C: EXOTOXIN TYPE A
D: EXOTOXIN TYPE A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,5428
Polymers103,2804
Non-polymers2624
Water2,450136
1
A: EXOTOXIN TYPE A
D: EXOTOXIN TYPE A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,7714
Polymers51,6402
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: EXOTOXIN TYPE A
C: EXOTOXIN TYPE A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,7714
Polymers51,6402
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)53.300, 127.200, 148.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.55652, 0.00048, 0.83084), (-0.00187, -1, -0.00067), (0.83083, -0.00193, 0.55652)-11.1864, 58.3731, 6.0632
2given(0.51999, -0.25207, -0.81614), (-0.23488, -0.96083, 0.1471), (-0.82125, 0.1152, -0.55882)44.4546, 54.50171, 65.76476
3given(-0.97083, 0.23899, -0.01936), (0.23916, 0.95943, -0.14934), (-0.01711, -0.14961, -0.9886)19.33516, 4.06527, 79.23849

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Components

#1: Protein
EXOTOXIN TYPE A / STREPTOCOCCAL PYOGENIC EXOTOXIN A1 / SPE A / SCARLET FEVER TOXIN / ERYTHROGENIC TOXIN


Mass: 25819.996 Da / Num. of mol.: 4 / Fragment: RESIDUES 31-251
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) STREPTOCOCCUS PYOGENES (bacteria) / Production host: ESCHERICHIA COLI BL21 (bacteria) / References: UniProt: P08095, UniProt: P0DJY7*PLUS
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 136 / Source method: isolated from a natural source / Formula: H2O
Compound detailsSUPERANTIGEN STEPTOCOCCAL PYROGENIC EXOTOXIN A1 IS RECOGNISED BY MHC CLASSII MOLECULES AND T-CELL ...SUPERANTIGEN STEPTOCOCCAL PYROGENIC EXOTOXIN A1 IS RECOGNISED BY MHC CLASSII MOLECULES AND T-CELL RECEPTORS. THE ZINC ION HAS BEEN SHOWN TO HAVE A ROLE AS A SECOND HIGH AFFINITY MHC CLASS II BINDING SITE AND IN THE THERMOSTABILITY OF SUPERANTIGENS.
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: 2.43 Å3/Da / Density % sol: 49.36 %
Crystal growpH: 6.5 / Details: pH 6.50

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX14.2 / Wavelength: 0.979
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.6→40 Å / Num. obs: 31727 / % possible obs: 89.8 % / Redundancy: 15.2 % / Rmerge(I) obs: 0.129 / Net I/σ(I): 16.6

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1B1Z

1b1z


Resolution: 2.6→20 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2822 1360 4.3 %RANDOM
Rwork0.2152 ---
obs0.2152 28046 89 %-
Solvent computationSolvent model: FLAT MODEL
Refinement stepCycle: LAST / Resolution: 2.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7248 0 4 136 7388
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.37
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ION.PARAMION.TOP
X-RAY DIFFRACTION3WATER_REP.PARAM

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