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- PDB-1an8: CRYSTAL STRUCTURE OF THE STREPTOCOCCAL SUPERANTIGEN SPE-C -

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Basic information

Entry
Database: PDB / ID: 1an8
TitleCRYSTAL STRUCTURE OF THE STREPTOCOCCAL SUPERANTIGEN SPE-C
ComponentsSTREPTOCOCCAL PYROGENIC EXOTOXIN C
KeywordsBACTERIAL SUPERANTIGEN / TOXIN
Function / homology
Function and homology information


toxin activity / extracellular region
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/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 ...Staphylococcal enterotoxin/Streptococcal pyrogenic exotoxin signature 1. / Staphylococcal/streptococcal toxin, bacterial / 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 C / Exotoxin type C
Similarity search - Component
Biological speciesStreptococcus pyogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.4 Å
AuthorsRoussel, A. / Baker, E.N.
CitationJournal: Nat.Struct.Biol. / Year: 1997
Title: Crystal structure of the streptococcal superantigen SPE-C: dimerization and zinc binding suggest a novel mode of interaction with MHC class II molecules.
Authors: Roussel, A. / Anderson, B.F. / Baker, H.M. / Fraser, J.D. / Baker, E.N.
History
DepositionJun 27, 1997Processing site: BNL
Revision 1.0Apr 29, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: STREPTOCOCCAL PYROGENIC EXOTOXIN C


Theoretical massNumber of molelcules
Total (without water)24,3841
Polymers24,3841
Non-polymers00
Water2,522140
1
A: STREPTOCOCCAL PYROGENIC EXOTOXIN C

A: STREPTOCOCCAL PYROGENIC EXOTOXIN C


Theoretical massNumber of molelcules
Total (without water)48,7692
Polymers48,7692
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Unit cell
Length a, b, c (Å)75.410, 75.410, 168.870
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein STREPTOCOCCAL PYROGENIC EXOTOXIN C / SPE-C


Mass: 24384.285 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pyogenes (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: P13380, UniProt: Q8NKX2*PLUS
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 140 / Source method: isolated from a natural source / Formula: H2O

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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: 4.98 Å3/Da / Density % sol: 75.01 %
Crystal growpH: 8
Details: PROTEIN WAS CRYSTALLIZED FROM 2.7 M AMMONIUM SULFATE IN 0.1 M TRIS/HCL BUFFER AT PH 8.0
Crystal grow
*PLUS
Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
15.5 mg/mlprotein1drop
20.1 Mphosphate1drop
32.7 Mammonium sulfate1reservoir
40.1 MTris-HCl1reservoir

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Type: PHOTON FACTORY / Wavelength: 1
DetectorType: FILM / Detector: FILM / Date: Apr 1, 1996
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→20 Å / Num. obs: 17866 / % possible obs: 91.6 % / Observed criterion σ(I): 2 / Redundancy: 3.5 % / Biso Wilson estimate: 34.317 Å2 / Rsym value: 0.103 / Net I/σ(I): 5.9
Reflection shellResolution: 2.42→2.57 Å / Redundancy: 3.6 % / Mean I/σ(I) obs: 2.4 / Rsym value: 0.325 / % possible all: 87.4
Reflection
*PLUS
Num. measured all: 71127 / Rmerge(I) obs: 0.103
Reflection shell
*PLUS
% possible obs: 87.4 % / Rmerge(I) obs: 0.423 / Mean I/σ(I) obs: 1.6

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Processing

Software
NameVersionClassification
CCP4model building
TNT5Erefinement
DENZOdata reduction
CCP4(ROTAVATA)data scaling
CCP4phasing
RefinementMethod to determine structure: MIR / Resolution: 2.4→20 Å / Isotropic thermal model: TNT BCORREL V1.0 / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
Details: X-PLOR ALSO WAS USED. RESIDUE 3 HAS NO REPORTED DENSITY.
RfactorNum. reflection% reflectionSelection details
Rfree0.21 1221 7 %RANDOM
Rwork0.171 ---
all0.174 17866 --
obs0.174 16645 91 %-
Solvent computationSolvent model: TRONRUD METHOD / Bsol: 189.6 Å2 / ksol: 0.734 e/Å3
Refinement stepCycle: LAST / Resolution: 2.4→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1702 0 0 140 1842
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.0117391.2
X-RAY DIFFRACTIONt_angle_deg1.26623391.3
X-RAY DIFFRACTIONt_dihedral_angle_d22.12710310
X-RAY DIFFRACTIONt_incorr_chiral_ct0
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.009522
X-RAY DIFFRACTIONt_gen_planes0.0142465
X-RAY DIFFRACTIONt_it2.66817394
X-RAY DIFFRACTIONt_nbd0.0332710
Software
*PLUS
Name: TNT / Version: 5E / Classification: refinement
Refinement
*PLUS
Rfactor Rfree: 0.215
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 28.1 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealWeight
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_dihedral_angle_deg22.1270
X-RAY DIFFRACTIONt_planar_d0.0092
X-RAY DIFFRACTIONt_plane_restr0.0145

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