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- PDB-3byt: A complex between a variant of staphylococcal enterotoxin C3 and ... -

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Basic information

Entry
Database: PDB / ID: 3byt
TitleA complex between a variant of staphylococcal enterotoxin C3 and the variable domain of the murine T cell receptor beta chain 8.2
Components
  • Enterotoxin type C-3
  • T cell receptor beta chain 8.2
KeywordsTOXIN / Secreted / Superantigen
Function / homology
Function and homology information


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/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) / Immunoglobulins / Roll / Immunoglobulin-like / Beta Barrel / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Enterotoxin type C-3
Similarity search - Component
Biological speciesMus musculus (house mouse)
Staphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.3 Å
AuthorsCho, S. / Eric, J.S.
CitationJournal: To be Published
Title: Manipulating the coupled folding and binding process drives affinity maturation in a protein-protein complex
Authors: Cho, S. / Swaminathan, C.P. / Kerzic, M.C. / Guan, R. / Yang, J. / Kieke, M.C. / Andersen, P.S. / Krantz, D.M. / Mariuzza, R.A. / Eric, S.J.
History
DepositionJan 16, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 12, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: T cell receptor beta chain 8.2
B: Enterotoxin type C-3
C: T cell receptor beta chain 8.2
D: Enterotoxin type C-3
E: T cell receptor beta chain 8.2
F: Enterotoxin type C-3
G: T cell receptor beta chain 8.2
H: Enterotoxin type C-3


Theoretical massNumber of molelcules
Total (without water)158,2368
Polymers158,2368
Non-polymers00
Water2,630146
1
A: T cell receptor beta chain 8.2
B: Enterotoxin type C-3


Theoretical massNumber of molelcules
Total (without water)39,5592
Polymers39,5592
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
C: T cell receptor beta chain 8.2
D: Enterotoxin type C-3


Theoretical massNumber of molelcules
Total (without water)39,5592
Polymers39,5592
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
E: T cell receptor beta chain 8.2
F: Enterotoxin type C-3


Theoretical massNumber of molelcules
Total (without water)39,5592
Polymers39,5592
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
G: T cell receptor beta chain 8.2
H: Enterotoxin type C-3


Theoretical massNumber of molelcules
Total (without water)39,5592
Polymers39,5592
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)63.157, 70.638, 98.843
Angle α, β, γ (deg.)74.780, 75.160, 88.260
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
T cell receptor beta chain 8.2


Mass: 11765.953 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli)
#2: Protein
Enterotoxin type C-3 / SEC3


Mass: 27793.133 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: entC3 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A0L5
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 146 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsRESIDUES 128-133 (VGKVTG) OF UNP ENTRY P0A0L5 WERE REPLACED WITH RESIDUES 100-104 (KASTWH) IN ...RESIDUES 128-133 (VGKVTG) OF UNP ENTRY P0A0L5 WERE REPLACED WITH RESIDUES 100-104 (KASTWH) IN CHAINS B,D,F,AND H OF THE CRYSTALLIZED SEQUENCE.

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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: 2.61 Å3/Da / Density % sol: 52.8 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 20% PEG 3350, 0.2 M tri-ammonium citrate pH 7.0, 0.3 % dioxane, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12B / Wavelength: 1.0722 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 21, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0722 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 96702 / Num. obs: 92210 / % possible obs: 90.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: 37.8 Å2 / Rmerge(I) obs: 0.047

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PDB_EXTRACT3.004data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementResolution: 2.3→30 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.905 / SU B: 11.535 / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.402 / ESU R Free: 0.275 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.278 3424 5.1 %RANDOM
Rwork0.226 ---
all0.234 67351 --
obs0.228 67140 95.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 43.566 Å2
Baniso -1Baniso -2Baniso -3
1-2.02 Å2-0.64 Å20.07 Å2
2--0.06 Å20.38 Å2
3----2.28 Å2
Refinement stepCycle: LAST / Resolution: 2.3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10908 0 0 146 11054
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0380.02211154
X-RAY DIFFRACTIONr_angle_refined_deg2.871.94415055
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.19851347
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.30225.137547
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.782151943
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.0461532
X-RAY DIFFRACTIONr_chiral_restr0.1740.21591
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.028512
X-RAY DIFFRACTIONr_nbd_refined0.2930.24729
X-RAY DIFFRACTIONr_nbtor_refined0.3310.27196
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2150.2404
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.330.257
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.310.28
X-RAY DIFFRACTIONr_mcbond_it1.851.57114
X-RAY DIFFRACTIONr_mcangle_it2.877210884
X-RAY DIFFRACTIONr_scbond_it3.97234951
X-RAY DIFFRACTIONr_scangle_it5.3684.54171
LS refinement shellResolution: 2.3→2.359 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.436 229 -
Rwork0.369 4177 -
all-4406 -
obs--85.21 %

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