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- PDB-3bzd: Manipulating the coupled folding and binding process drives affin... -

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Basic information

Entry
Database: PDB / ID: 3bzd
TitleManipulating the coupled folding and binding process drives affinity maturation in a protein-protein complex
Components
  • Enterotoxin type C-3
  • T cell receptor beta chain 8.2
KeywordsTOXIN / Superantigen / Secreted
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 enterotoxin/Streptococcal pyrogenic exotoxin, conserved site / Staphyloccocal enterotoxin/Streptococcal pyrogenic exotoxin signature 2. / Superantigen, staphylococcal/streptococcal toxin, bacterial / Staphylococcal/Streptococcal toxin, beta-grasp domain / Staphylococcal/Streptococcal toxin, beta-grasp domain / 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 enterotoxin/Streptococcal pyrogenic exotoxin, conserved site / Staphyloccocal enterotoxin/Streptococcal pyrogenic exotoxin signature 2. / Superantigen, staphylococcal/streptococcal toxin, bacterial / Staphylococcal/Streptococcal toxin, beta-grasp domain / Staphylococcal/Streptococcal toxin, beta-grasp domain / 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 / Resolution: 2.3 Å
AuthorsCho, 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 17, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 12, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _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: T cell receptor beta chain 8.2
B: Enterotoxin type C-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,6484
Polymers39,4562
Non-polymers1922
Water1,53185
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)96.970, 96.970, 92.510
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65

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Components

#1: Protein T cell receptor beta chain 8.2


Mass: 11765.953 Da / Num. of mol.: 1 / Fragment: Variable domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: PT7-7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
#2: Protein Enterotoxin type C-3 / SEC3


Mass: 27690.033 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: entC3 / Plasmid: PET26b+ / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P0A0L5
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 85 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsRESIDUES 129-133 (GKVTG) OF UNP ENTRY P0A0L5 WERE REPLACED WITH RESIDUES 102-104 (WWH) IN THE ...RESIDUES 129-133 (GKVTG) OF UNP ENTRY P0A0L5 WERE REPLACED WITH RESIDUES 102-104 (WWH) IN 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: 3.21 Å3/Da / Density % sol: 61.64 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 2.0 M ammonium sulfate, 0.1 M Tris-Cl pH 7.0, 0.3 % 1,6-diaminohexane, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Mar 15, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / Num. all: 23532 / Num. obs: 21938 / % possible obs: 99.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: 31.3 Å2 / Rmerge(I) obs: 0.058
Reflection shellResolution: 2.3→2.36 Å / Rmerge(I) obs: 0.356 / Num. unique all: 1518 / % possible all: 93.3

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PDB_EXTRACT3.004data extraction
CrystalCleardata collection
CrystalCleardata reduction
CrystalCleardata scaling
MOLREPphasing
RefinementResolution: 2.3→27.99 Å / Cor.coef. Fo:Fc: 0.903 / Cor.coef. Fo:Fc free: 0.865 / SU B: 9.004 / SU ML: 0.217 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.27 / ESU R Free: 0.223 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.258 1073 4.9 %RANDOM
Rwork0.21 ---
obs0.213 21938 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.38 Å2
Baniso -1Baniso -2Baniso -3
1-1.51 Å20.76 Å20 Å2
2--1.51 Å20 Å2
3----2.27 Å2
Refinement stepCycle: LAST / Resolution: 2.3→27.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2755 0 10 85 2850
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0310.0222827
X-RAY DIFFRACTIONr_angle_refined_deg2.3591.9443819
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8875339
X-RAY DIFFRACTIONr_dihedral_angle_2_deg44.20125.108139
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.36715491
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.678158
X-RAY DIFFRACTIONr_chiral_restr0.1580.2401
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.022151
X-RAY DIFFRACTIONr_nbd_refined0.3260.21494
X-RAY DIFFRACTIONr_nbtor_refined0.3430.21900
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2440.2184
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2990.243
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1230.26
X-RAY DIFFRACTIONr_mcbond_it1.6631.51759
X-RAY DIFFRACTIONr_mcangle_it2.43522739
X-RAY DIFFRACTIONr_scbond_it3.91131271
X-RAY DIFFRACTIONr_scangle_it4.764.51080
LS refinement shellResolution: 2.3→2.359 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.327 75 -
Rwork0.31 1518 -
all-1593 -
obs--100 %

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