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- PDB-1cqf: THE COMPLEX OF THE MUTATED SHIGA TOXIN B SUBUNIT AND GB3 TRISACCHARIDE -

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Basic information

Entry
Database: PDB / ID: 1cqf
TitleTHE COMPLEX OF THE MUTATED SHIGA TOXIN B SUBUNIT AND GB3 TRISACCHARIDE
ComponentsSHIGA TOXIN B-CHAIN
KeywordsTOXIN / BACTERIAL TOXIN / SUGAR RECEPTOR BINDING DOMAIN / PROTEIN-CARBOHYDRATE RECOGNITION / OB-FOLD
Function / homology
Function and homology information


symbiont-mediated modulation of host virulence / hemolysis by symbiont of host erythrocytes / toxin activity / extracellular region
Similarity search - Function
OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #70 / Shiga-like toxin, beta subunit / Shiga-like toxin beta subunit / Enterotoxin / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Shiga-like toxin 1 subunit B / Shiga-like toxin 1 subunit B
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / Resolution: 2.2 Å
AuthorsLing, H. / Bast, D. / Brunton, J.L. / Read, R.J.
CitationJournal: To be Published
Title: The Complex of the Mutated Shiga Toxin B Subunit and Gb3 Trisaccharide
Authors: Ling, H. / Bast, D. / Brunton, J.L. / Read, R.J.
History
DepositionAug 6, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 7, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / 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 / struct_asym / struct_conn / 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 / _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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 3, 2021Group: Database references / Structure summary / Category: chem_comp / database_2 / struct_ref_seq_dif
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SHIGA TOXIN B-CHAIN
B: SHIGA TOXIN B-CHAIN
C: SHIGA TOXIN B-CHAIN
D: SHIGA TOXIN B-CHAIN
E: SHIGA TOXIN B-CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,74011
Polymers38,7135
Non-polymers3,0276
Water2,054114
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.785, 73.561, 83.853
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
SHIGA TOXIN B-CHAIN


Mass: 7742.686 Da / Num. of mol.: 5 / Fragment: SHIGA-LIKE TOXIN I BINDING DOMAIN / Mutation: G62T
Source method: isolated from a genetically manipulated source
Details: COMPLEXED WITH TRISACCHARIDE OF GLYCOLIPID GB3 / Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: P08027, UniProt: P69179*PLUS
#2: Polysaccharide
alpha-D-galactopyranose-(1-4)-beta-D-galactopyranose-(1-4)-beta-D-glucopyranose


Type: oligosaccharide / Mass: 504.438 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGalpa1-4DGalpb1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,3,2/[a2122h-1b_1-5][a2112h-1b_1-5][a2112h-1a_1-5]/1-2-3/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][b-D-Galp]{[(4+1)][a-D-Galp]{}}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 114 / Source method: isolated from a natural source / Formula: H2O

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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: 2.5 Å3/Da / Density % sol: 50.81 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.2 M CaCl2, 26% PEG 400, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: MACSCIENCE / Detector: IMAGE PLATE / Date: Nov 20, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→19.8 Å / Num. all: 20327 / Num. obs: 18719 / % possible obs: 92.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 1.5 % / Biso Wilson estimate: 15.3 Å2 / Rmerge(I) obs: 0.052 / Net I/σ(I): 16.76
Reflection shellResolution: 2.2→2.23 Å / Redundancy: 1.3 % / Rmerge(I) obs: 0.228 / Num. unique all: 773 / % possible all: 75.7

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
RefinementResolution: 2.2→19.8 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: through maximum likelihood F target, with NCS restraints.
RfactorNum. reflection% reflectionSelection details
Rfree0.2 1040 5.1 %thin shells through whole resolution range
Rwork0.181 ---
all0.181 20327 --
obs0.181 18719 92.1 %-
Refinement stepCycle: LAST / Resolution: 2.2→19.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2715 0 204 114 3033
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.04

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