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- PDB-3dwa: Crystal structure of the B-subunit of the AB5 toxin from E. coli -

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Basic information

Entry
Database: PDB / ID: 3dwa
TitleCrystal structure of the B-subunit of the AB5 toxin from E. coli
ComponentsSubtilase cytotoxin, subunit B
KeywordsTOXIN
Function / homologyOB fold (Dihydrolipoamide Acetyltransferase, E2P) - #110 / Enterotoxin / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Beta Barrel / Mainly Beta / identical protein binding / Subtilase SubB
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.084 Å
AuthorsByres, E. / Paton, A.W. / Paton, J.C. / Lofling, J.C. / Smith, D.F. / Wilce, M.C.J. / Talbot, U.M. / Chong, D.C. / Yu, H. / Huang, S. ...Byres, E. / Paton, A.W. / Paton, J.C. / Lofling, J.C. / Smith, D.F. / Wilce, M.C.J. / Talbot, U.M. / Chong, D.C. / Yu, H. / Huang, S. / Chen, X. / Varki, N.M. / Varki, A. / Rossjohn, J. / Beddoe, T.
CitationJournal: Nature / Year: 2008
Title: Incorporation of a non-human glycan mediates human susceptibility to a bacterial toxin
Authors: Byres, E. / Paton, A.W. / Paton, J.C. / Lofling, J.C. / Smith, D.F. / Wilce, M.C.J. / Talbot, U.M. / Chong, D.C. / Yu, H. / Huang, S. / Chen, X. / Varki, N.M. / Varki, A. / Rossjohn, J. / Beddoe, T.
History
DepositionJul 22, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 4, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Subtilase cytotoxin, subunit B
B: Subtilase cytotoxin, subunit B
C: Subtilase cytotoxin, subunit B
D: Subtilase cytotoxin, subunit B
E: Subtilase cytotoxin, subunit B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,82810
Polymers70,6375
Non-polymers1,1915
Water6,125340
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13110 Å2
ΔGint-59 kcal/mol
Surface area22150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.63, 97.63, 165.36
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein
Subtilase cytotoxin, subunit B / SubB


Mass: 14127.389 Da / Num. of mol.: 5 / Fragment: residues in database 24-141
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: subB / Production host: Escherichia coli (E. coli) / References: UniProt: Q3ZTX8
#2: Chemical
ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 340 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.22 Å3/Da / Density % sol: 61.81 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: 16%(w/v) PEG 3350, 100mM sodium cacodylate, 200mM ammonium fluoride, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-ID-B
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.084→84.22 Å / Num. obs: 45985
Reflection shellHighest resolution: 2.084 Å

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Processing

SoftwareName: REFMAC / Version: 5.2.0019 / Classification: refinement
RefinementMethod to determine structure: SAD / Resolution: 2.084→48.8 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.922 / SU B: 3.912 / SU ML: 0.107 / Cross valid method: THROUGHOUT / ESU R: 0.192 / ESU R Free: 0.177 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.23626 2361 5.1 %RANDOM
Rwork0.1894 ---
obs0.19182 43610 86.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.1 Å2
Baniso -1Baniso -2Baniso -3
1--0.98 Å2-0.49 Å20 Å2
2---0.98 Å20 Å2
3---1.48 Å2
Refinement stepCycle: LAST / Resolution: 2.084→48.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4546 0 80 340 4966
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0224758
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7021.9416442
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.3875583
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.23523.846195
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.59715705
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.2971515
X-RAY DIFFRACTIONr_chiral_restr0.1280.2679
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023592
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2160.22193
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3080.23257
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1670.2321
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2730.238
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1280.24
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3931.52978
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.04524699
X-RAY DIFFRACTIONr_scbond_it3.01132104
X-RAY DIFFRACTIONr_scangle_it4.2934.51743
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.084→2.138 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.288 144 -
Rwork0.22 2622 -
obs-518836 71.53 %

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