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- PDB-3dwp: Crystal structure of the B-subunit of the AB5 toxin from E. Coli ... -

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Basic information

Entry
Database: PDB / ID: 3dwp
TitleCrystal structure of the B-subunit of the AB5 toxin from E. Coli with Neu5Gc
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 / N-glycolyl-alpha-neuraminic acid / Subtilase SubB
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 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
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id

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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)72,98615
Polymers70,1685
Non-polymers2,81810
Water8,647480
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13160 Å2
ΔGint-59 kcal/mol
Surface area21860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.900, 96.900, 165.622
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLU / Beg label comp-ID: GLU / End auth comp-ID: LYS / End label comp-ID: LYS / Refine code: 4 / Auth seq-ID: 1 - 115 / Label seq-ID: 1 - 115

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD
5EE

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Components

#1: Protein
Subtilase cytotoxin, subunit B / SubB


Mass: 14033.598 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: Sugar
ChemComp-NGC / N-glycolyl-alpha-neuraminic acid / N-glycolylneuraminic acid / sialic acid / 3,5-dideoxy-5-[(hydroxyacetyl)amino]-D-glycero-alpha-D-galacto-non-2-ulopyranosonic acid


Type: D-saccharide, alpha linking / Mass: 325.269 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Formula: C11H19NO10
IdentifierTypeProgram
DNeup5GcaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-glycolyl-a-D-neuraminic acidCOMMON NAMEGMML 1.0
a-D-Neup5GcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
Neu5GcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical
ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


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


Mass: 18.015 Da / Num. of mol.: 480 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.2 Å3/Da / Density % sol: 61.55 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: 16% 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: ROTATING ANODE / Type: RIGAKU RUH3R
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.2→83.92 Å / Num. obs: 39693
Reflection shellResolution: 2.2→2.32 Å

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Processing

SoftwareName: REFMAC / Version: 5.2.0019 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→23.97 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.909 / SU B: 5.134 / SU ML: 0.131 / Cross valid method: THROUGHOUT / ESU R: 0.243 / ESU R Free: 0.208 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.23992 2019 5.1 %RANDOM
Rwork0.18818 ---
obs0.19081 37666 89.04 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.463 Å2
Baniso -1Baniso -2Baniso -3
1--0.6 Å2-0.3 Å20 Å2
2---0.6 Å20 Å2
3---0.9 Å2
Refinement stepCycle: LAST / Resolution: 2.2→23.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4532 0 190 480 5202
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0224857
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4681.9656589
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1625581
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.92223.814194
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.07815703
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.3771515
X-RAY DIFFRACTIONr_chiral_restr0.0950.2708
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023625
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1990.22340
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3030.23295
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1720.2393
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2040.260
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2030.210
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7041.52959
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.20524685
X-RAY DIFFRACTIONr_scbond_it1.62932205
X-RAY DIFFRACTIONr_scangle_it2.5694.51904
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 884 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Amedium positional0.330.5
2Bmedium positional0.40.5
3Cmedium positional0.360.5
4Dmedium positional0.40.5
5Emedium positional0.370.5
1Amedium thermal0.922
2Bmedium thermal0.912
3Cmedium thermal0.862
4Dmedium thermal0.822
5Emedium thermal0.782
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.298 160 -
Rwork0.233 2905 -
obs--93.19 %

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