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

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Basic information

Entry
Database: PDB / ID: 3bvm
TitleManipulating the coupled folding and binding process drives affinity maturation in a protein-protein complex
ComponentsEnterotoxin type C-3
KeywordsTOXIN / N-terminal Oligosaccharide/oligonucleotide fold / Enterotoxin / 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 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) / Roll / Beta Barrel / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Enterotoxin type C-3
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2 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 7, 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_ref_seq_dif / 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_ref_seq_dif.details / _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: Enterotoxin type C-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,7442
Polymers27,6791
Non-polymers651
Water4,107228
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.619, 42.619, 286.523
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-339-

HOH

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Components

#1: Protein Enterotoxin type C-3 / SEC3


Mass: 27679.051 Da / Num. of mol.: 1
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
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 228 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsRESIDUES 128-133 (VGKVTG) OF UNP ENTRY P0A0L5 WERE REPLACED WITH RESIDUES 103-106 (KWWP) IN THE ...RESIDUES 128-133 (VGKVTG) OF UNP ENTRY P0A0L5 WERE REPLACED WITH RESIDUES 103-106 (KWWP) 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: 2.37 Å3/Da / Density % sol: 48.02 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: containing 0.1M Tris-Cl, pH 8.5, 2.4 M ammonium sulfate, 2.25% polyethylene glycol (PEG) 400 and 2.25% Tween 20, 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: May 24, 2004 / Details: mirrors
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 17009 / % possible obs: 89 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: 30.6 Å2 / Rmerge(I) obs: 0.073

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0005refinement
PDB_EXTRACT3.004data extraction
CrystalCleardata collection
CrystalCleardata reduction
CrystalCleardata scaling
MOLREPphasing
RefinementResolution: 2→30 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.849 / SU B: 6.279 / SU ML: 0.177 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.24 / ESU R Free: 0.246 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.274 857 5 %RANDOM
Rwork0.22 ---
all0.231 ---
obs0.225 17009 88.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.899 Å2
Baniso -1Baniso -2Baniso -3
1-0.25 Å20 Å20 Å2
2--0.25 Å20 Å2
3----0.51 Å2
Refinement stepCycle: LAST / Resolution: 2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1853 0 1 228 2082
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0221894
X-RAY DIFFRACTIONr_angle_refined_deg1.9121.952553
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6895224
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.06825.81698
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.44915348
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.667153
X-RAY DIFFRACTIONr_chiral_restr0.1320.2269
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021439
X-RAY DIFFRACTIONr_nbd_refined0.2480.2965
X-RAY DIFFRACTIONr_nbtor_refined0.3090.21243
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2210.2215
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2530.235
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2080.212
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.1520.21
X-RAY DIFFRACTIONr_mcbond_it1.2011.51166
X-RAY DIFFRACTIONr_mcangle_it1.89921822
X-RAY DIFFRACTIONr_scbond_it2.8623861
X-RAY DIFFRACTIONr_scangle_it4.1284.5731
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.364 49 -
Rwork0.276 1064 -
all-1113 -
obs--81.24 %

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