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- PDB-1ha5: Structural features of a zinc-binding site in the superantigen st... -

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Basic information

Entry
Database: PDB / ID: 1ha5
TitleStructural features of a zinc-binding site in the superantigen streptococcal pyrogenic exotoxin A (SpeA1): implications for MHC class II recognition.
ComponentsSTREPTOCOCCAL PYOGENIC EXOTOXIN A1
KeywordsTOXIN / MOLECULAR RECOGNITION / SUPERANTIGEN / EXOTOXIN / ZINC BINDING
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/Streptococcal toxin, beta-grasp domain / Staphylococcal/Streptococcal toxin, beta-grasp domain / Staphylococcal enterotoxin/Streptococcal pyrogenic exotoxin, conserved site / Staphyloccocal enterotoxin/Streptococcal pyrogenic exotoxin signature 2. / Superantigen, staphylococcal/streptococcal toxin, bacterial / Ubiquitin-like (UB roll) - #120 / Superantigen toxin, C-terminal ...Staphylococcal enterotoxin/Streptococcal pyrogenic exotoxin signature 1. / Staphylococcal/Streptococcal toxin, OB-fold / Staphylococcal/Streptococcal toxin, OB-fold domain / Staphylococcal/Streptococcal toxin, beta-grasp domain / Staphylococcal/Streptococcal toxin, beta-grasp domain / Staphylococcal enterotoxin/Streptococcal pyrogenic exotoxin, conserved site / Staphyloccocal enterotoxin/Streptococcal pyrogenic exotoxin signature 2. / Superantigen, staphylococcal/streptococcal toxin, bacterial / 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
Exotoxin type A / Exotoxin type A
Similarity search - Component
Biological speciesSTREPTOCOCCUS PYOGENES (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.82 Å
AuthorsBaker, M.D. / Gutman, D.M. / Papageorgiou, A.C. / Collins, C.M. / Acharya, K.R.
CitationJournal: Protein Sci. / Year: 2001
Title: Structural Features of a Zinc Binding Site in the Superantigen Strepococcal Pyrogenic Exotoxin a (Spea1): Implications for Mhc Class II Recognition.
Authors: Baker, M.D. / Gutman, D.M. / Papageorgiou, A.C. / Collins, C.M. / Acharya, K.R.
History
DepositionMar 28, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 3, 2002Provider: repository / Type: Initial release
Revision 1.1May 7, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 24, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
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 / 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.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 / _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

Downloads & links

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Assembly

Deposited unit
A: STREPTOCOCCAL PYOGENIC EXOTOXIN A1
B: STREPTOCOCCAL PYOGENIC EXOTOXIN A1
C: STREPTOCOCCAL PYOGENIC EXOTOXIN A1
D: STREPTOCOCCAL PYOGENIC EXOTOXIN A1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,7688
Polymers101,5064
Non-polymers2624
Water2,558142
1
A: STREPTOCOCCAL PYOGENIC EXOTOXIN A1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,4422
Polymers25,3771
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: STREPTOCOCCAL PYOGENIC EXOTOXIN A1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,4422
Polymers25,3771
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: STREPTOCOCCAL PYOGENIC EXOTOXIN A1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,4422
Polymers25,3771
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: STREPTOCOCCAL PYOGENIC EXOTOXIN A1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,4422
Polymers25,3771
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)126.946, 101.320, 82.019
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.81858, 0.38074, 0.43008), (0.38661, -0.91897, 0.0777), (0.42481, 0.10267, -0.89944)-27.65683, 117.6848, 10.46601
2given(-0.88628, -0.45384, -0.09243), (-0.4596, 0.83708, 0.29676), (-0.05731, 0.30549, -0.95047)213.83876, 46.25376, 40.28626
3given(-0.93229, 0.06627, -0.35559), (0.08612, -0.91414, -0.39614), (-0.35131, -0.39994, 0.84654)183.98863, 159.65471, 69.67257

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Components

#1: Protein
STREPTOCOCCAL PYOGENIC EXOTOXIN A1


Mass: 25376.520 Da / Num. of mol.: 4 / Fragment: RESIDUES 33-250
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) STREPTOCOCCUS PYOGENES (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / 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.: 142 / 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.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.6 Å3/Da / Density % sol: 52.66 %
Crystal growpH: 6.5 / Details: pH 6.50

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.9057
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9057 Å / Relative weight: 1
ReflectionResolution: 2.8→40 Å / Num. obs: 26185 / % possible obs: 95.8 % / Redundancy: 5.7 % / Biso Wilson estimate: 5.7 Å2 / Rmerge(I) obs: 0.108 / Net I/σ(I): 6.4
Reflection shellResolution: 2.8→2.9 Å / Rmerge(I) obs: 0.285 / Mean I/σ(I) obs: 5.3 / % possible all: 61.3

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Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1B1Z

1b1z


Resolution: 2.82→39.6 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1727947.22 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: RESIDUES 5, 88, 112, 115, 179, 180 WERE MODELLED AS ALANINE IN ALL 4 MOLECULES DUE TO INSUFFICIENT DENSITY.
RfactorNum. reflection% reflectionSelection details
Rfree0.2834 2482 9.9 %RANDOM
Rwork0.214 ---
obs0.214 25045 95.3 %-
Solvent computationSolvent model: FLAT MODEL / ksol: 0.317447 e/Å3
Displacement parametersBiso mean: 31.1 Å2
Baniso -1Baniso -2Baniso -3
1--6 Å20 Å20 Å2
2---0.19 Å20 Å2
3---6.19 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.5 Å0.38 Å
Luzzati d res low-5 Å
Luzzati sigma a0.51 Å0.45 Å
Refinement stepCycle: LAST / Resolution: 2.82→39.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7034 0 4 142 7180
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_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.86
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
LS refinement shellResolution: 2.82→2.98 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.388 286 10.3 %
Rwork0.325 2494 -
obs--63.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ION.PARAM
X-RAY DIFFRACTION3WATER_REP.PARAM

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