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- PDB-3dwq: Crystal structure of the A-subunit of the AB5 toxin from E. coli ... -

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Basic information

Entry
Database: PDB / ID: 3dwq
TitleCrystal structure of the A-subunit of the AB5 toxin from E. coli with Neu5Gc-2,3Gal-1,3GlcNAc
ComponentsSubtilase cytotoxin, subunit BAB5 toxin
KeywordsTOXIN
Function / homologyOB fold (Dihydrolipoamide Acetyltransferase, E2P) - #110 / Enterotoxin / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Beta Barrel / Mainly Beta / identical protein binding / AZIDE ION / N-PROPANOL / Subtilase SubB
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 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: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_validate_chiral / pdbx_validate_close_contact / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_atom_id / _pdbx_validate_chiral.auth_comp_id / _pdbx_validate_chiral.auth_seq_id / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_atom_id_1 / _pdbx_validate_close_contact.auth_atom_id_2 / _pdbx_validate_close_contact.auth_comp_id_1 / _pdbx_validate_close_contact.auth_comp_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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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)74,53022
Polymers70,1685
Non-polymers4,36217
Water10,016556
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15910 Å2
ΔGint-15 kcal/mol
Surface area23180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.253, 97.253, 163.520
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 label comp-ID: GLU / 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

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Protein / Sugars , 2 types, 9 molecules ABCDE

#1: Protein
Subtilase cytotoxin, subunit B / AB5 toxin / 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: Polysaccharide
N-glycolyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-galactopyranose


Type: oligosaccharide / Mass: 690.603 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DNeup5Gca2-3DGalpb1-3DGalpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,3,2/[a2112h-1b_1-5_2*NCC/3=O][a2112h-1b_1-5][Aad21122h-2a_2-6_5*NCCO/3=O]/1-2-3/a3-b1_b3-c2WURCSPDB2Glycan 1.1.0
[][L-1-deoxy-GalpNAc]{[(3+1)][b-L-Galp]{[(3+2)]{}}}LINUCSPDB-CARE

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Non-polymers , 4 types, 569 molecules

#3: Chemical
ChemComp-POL / N-PROPANOL / 1-PROPONOL / Propan-1-ol


Mass: 60.095 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O
#4: Chemical
ChemComp-AZI / AZIDE ION / Azide


Mass: 42.020 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: N3
#5: Chemical
ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400 / Polyethylene glycol


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


Mass: 18.015 Da / Num. of mol.: 556 / 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: 3.18 Å3/Da / Density % sol: 61.34 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: 16% PEG 3350, 100mM sodium cacodylate, pH 6.2, 200mM ammonium fluoride, 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: 2.1→84.22 Å / Num. obs: 45181

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Processing

SoftwareName: REFMAC / Version: 5.2.0019 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→29.67 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.885 / SU B: 5.378 / SU ML: 0.142 / Cross valid method: THROUGHOUT / ESU R: 0.254 / ESU R Free: 0.216 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2615 2177 5.1 %RANDOM
Rwork0.21079 ---
obs0.21338 40527 83.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.623 Å2
Baniso -1Baniso -2Baniso -3
1--1.04 Å2-0.52 Å20 Å2
2---1.04 Å20 Å2
3---1.56 Å2
Refinement stepCycle: LAST / Resolution: 2.1→29.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4532 0 292 556 5380
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0224967
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5381.9896737
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.975581
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.82123.814194
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.50115703
X-RAY DIFFRACTIONr_dihedral_angle_4_deg7.7571515
X-RAY DIFFRACTIONr_chiral_restr0.2170.2742
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.023632
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1780.22411
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3010.23454
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1120.2505
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1850.266
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0610.28
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.3041.52973
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.53524685
X-RAY DIFFRACTIONr_scbond_it0.58932315
X-RAY DIFFRACTIONr_scangle_it1.0154.52052
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 positional0.290.5
2Bmedium positional0.390.5
3Cmedium positional0.310.5
4Dmedium positional0.340.5
5Emedium positional0.370.5
1Amedium thermal0.232
2Bmedium thermal0.222
3Cmedium thermal0.232
4Dmedium thermal0.172
5Emedium thermal0.222
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.336 156 -
Rwork0.27 3147 -
obs--87.85 %

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