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- PDB-1bos: SHIGA-LIKE TOXIN COMPLEXED WITH ITS RECEPTOR -

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Basic information

Entry
Database: PDB / ID: 1bos
TitleSHIGA-LIKE TOXIN COMPLEXED WITH ITS RECEPTOR
ComponentsSHIGA-LIKE TOXIN I B SUBUNIT
KeywordsTOXIN / RECEPTOR BINDING / PROTEIN-CARBOHYDRATE RECOGNITION / OB-FOLD
Function / homology
Function and homology information


symbiont-mediated modulation of host virulence / symbiont-mediated hemolysis of host erythrocyte / toxin activity / extracellular region
Similarity search - Function
Shiga-like toxin, beta subunit / Shiga-like toxin beta subunit / Enterotoxin
Similarity search - Domain/homology
beta-D-galactopyranose / Shiga-like toxin 1 subunit B / Shiga-like toxin 1 subunit B
Similarity search - Component
Biological speciesPhage h30 (virus)
Enterobacteria phage H-19B (virus)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsLing, H. / Boodhoo, A. / Hazes, B. / Cummings, M.D. / Armstrong, G.D. / Brunton, J.L. / Read, R.J.
Citation
Journal: Biochemistry / Year: 1998
Title: Structure of the shiga-like toxin I B-pentamer complexed with an analogue of its receptor Gb3.
Authors: Ling, H. / Boodhoo, A. / Hazes, B. / Cummings, M.D. / Armstrong, G.D. / Brunton, J.L. / Read, R.J.
#1: Journal: Nature / Year: 1992
Title: Crystal Structure of the Cell-Binding B Oligomer of Verotoxin-1 from E. Coli
Authors: Stein, P.E. / Boodhoo, A. / Tyrrell, G.J. / Brunton, J.L. / Read, R.J.
History
DepositionJan 13, 1998Processing site: BNL
Revision 1.0Feb 2, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 4, 2018Group: Advisory / Data collection / Other
Category: diffrn_source / pdbx_database_status / pdbx_unobs_or_zero_occ_atoms
Item: _diffrn_source.type / _pdbx_database_status.process_site
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / 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.occupancy / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_database_status.pdb_format_compatible / _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 2.1Aug 9, 2023Group: Advisory / Database references ...Advisory / Database references / Refinement description / Structure summary
Category: chem_comp / database_2 ...chem_comp / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Nov 6, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SHIGA-LIKE TOXIN I B SUBUNIT
B: SHIGA-LIKE TOXIN I B SUBUNIT
C: SHIGA-LIKE TOXIN I B SUBUNIT
D: SHIGA-LIKE TOXIN I B SUBUNIT
E: SHIGA-LIKE TOXIN I B SUBUNIT
F: SHIGA-LIKE TOXIN I B SUBUNIT
G: SHIGA-LIKE TOXIN I B SUBUNIT
H: SHIGA-LIKE TOXIN I B SUBUNIT
I: SHIGA-LIKE TOXIN I B SUBUNIT
J: SHIGA-LIKE TOXIN I B SUBUNIT
K: SHIGA-LIKE TOXIN I B SUBUNIT
L: SHIGA-LIKE TOXIN I B SUBUNIT
M: SHIGA-LIKE TOXIN I B SUBUNIT
N: SHIGA-LIKE TOXIN I B SUBUNIT
O: SHIGA-LIKE TOXIN I B SUBUNIT
P: SHIGA-LIKE TOXIN I B SUBUNIT
Q: SHIGA-LIKE TOXIN I B SUBUNIT
R: SHIGA-LIKE TOXIN I B SUBUNIT
S: SHIGA-LIKE TOXIN I B SUBUNIT
T: SHIGA-LIKE TOXIN I B SUBUNIT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)178,07880
Polymers153,97320
Non-polymers24,10560
Water6,215345
1
A: SHIGA-LIKE TOXIN I B SUBUNIT
B: SHIGA-LIKE TOXIN I B SUBUNIT
C: SHIGA-LIKE TOXIN I B SUBUNIT
D: SHIGA-LIKE TOXIN I B SUBUNIT
E: SHIGA-LIKE TOXIN I B SUBUNIT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,60020
Polymers38,4935
Non-polymers6,10715
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
F: SHIGA-LIKE TOXIN I B SUBUNIT
G: SHIGA-LIKE TOXIN I B SUBUNIT
H: SHIGA-LIKE TOXIN I B SUBUNIT
I: SHIGA-LIKE TOXIN I B SUBUNIT
J: SHIGA-LIKE TOXIN I B SUBUNIT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,60020
Polymers38,4935
Non-polymers6,10715
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
K: SHIGA-LIKE TOXIN I B SUBUNIT
L: SHIGA-LIKE TOXIN I B SUBUNIT
M: SHIGA-LIKE TOXIN I B SUBUNIT
N: SHIGA-LIKE TOXIN I B SUBUNIT
O: SHIGA-LIKE TOXIN I B SUBUNIT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,27620
Polymers38,4935
Non-polymers5,78315
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
P: SHIGA-LIKE TOXIN I B SUBUNIT
Q: SHIGA-LIKE TOXIN I B SUBUNIT
R: SHIGA-LIKE TOXIN I B SUBUNIT
S: SHIGA-LIKE TOXIN I B SUBUNIT
T: SHIGA-LIKE TOXIN I B SUBUNIT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,60020
Polymers38,4935
Non-polymers6,10715
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)127.500, 97.700, 164.200
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
22
33
/ NCS ensembles :
ID
1
2
3

NCS oper:
IDCodeMatrixVector
1given(0.321935, -0.730389, 0.602402), (0.75771, 0.580263, 0.298612), (-0.567655, 0.360313, 0.740231)57.909, -14.77, 9.159
2given(-0.799927, -0.441849, 0.406061), (0.502144, -0.122339, 0.856087), (-0.328584, 0.888708, 0.319734)93.24, 24.515, -22.197
3given(-0.804694, 0.494153, -0.329059), (-0.432479, -0.10819, 0.895129), (0.40673, 0.862617, 0.300771)55.187, 62.678, -51.787
4given(0.292481, 0.770761, -0.566024), (-0.732478, 0.561092, 0.385552), (0.61476, 0.301833, 0.728674)-2.095, 48.428, -37.666
5given(-0.994729, -0.081379, 0.062385), (-0.078416, 0.995737, 0.048567), (-0.066072, 0.043419, -0.99687)87.455, -46.091, 1.888
6given(-0.390227, 0.703271, -0.594249), (0.715786, 0.637679, 0.284632), (0.579114, -0.314284, -0.752231)30.419, -64.624, -10.043
7given(0.735073, 0.492312, -0.466151), (0.559572, -0.052323, 0.827128), (0.382815, -0.868845, -0.313945)-8.372, -30.23, 20.44
8given(0.86244, -0.429723, 0.267461), (-0.349417, -0.123156, 0.928838), (-0.366203, -0.894523, -0.256367)23.913, 10.388, 52.734
9given(-0.207725, -0.785847, 0.58249), (-0.735576, 0.518023, 0.436555), (-0.644808, -0.337783, -0.685656)83.135, 0.68, 41.747
10given(-0.643227, 0.703159, 0.303026), (0.764114, 0.564244, 0.312664), (0.048872, 0.432661, -0.900231)-3.088, -43.785, -60.396
11given(0.155286, 0.986423, 0.053433), (0.491097, -0.124016, 0.862232), (0.857152, -0.107652, -0.503687)-47.876, -4.352, -72.456
12given(0.772733, 0.465118, 0.431912), (-0.434285, -0.108831, 0.894177), (0.462904, -0.878533, 0.117896)-52.43, 33.515, -24.677
13given(0.342018, -0.127582, 0.930992), (-0.732628, 0.584219, 0.349205), (-0.588456, -0.801505, 0.106343)-10.58, 17.769, 16.119
14given(-0.513719, -0.001974, 0.857956), (0.009409, 0.999924, 0.007934), (-0.857907, 0.012148, -0.513661)20.41, -30.08, -5.622
15given(-0.679135, -0.702635, -0.212317), (-0.723227, 0.591146, 0.357056), (-0.125369, 0.396043, -0.909633)56.914, 15.658, 30.993
16given(-0.627596, 0.020274, -0.778275), (0.021004, 0.999738, 0.009105), (0.778256, -0.010633, -0.627857)25.41, -32.057, 9.726
17given(0.266968, 0.187985, -0.945193), (0.757364, 0.565565, 0.326399), (0.595926, -0.802993, 0.008614)-18.853, -45.309, 49.51
18given(0.755805, -0.444299, -0.480996), (0.476728, -0.13019, 0.869356), (-0.448876, -0.886368, 0.113411)-13.428, -5.163, 96.373
19given(0.17931, -0.983485, -0.024585), (-0.45002, -0.10422, 0.886916), (-0.874831, -0.147969, -0.461276)32.661, 32.517, 84.715

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Components

#1: Protein
SHIGA-LIKE TOXIN I B SUBUNIT


Mass: 7698.634 Da / Num. of mol.: 20 / Fragment: RECEPTOR-BINDING DOMAIN
Source method: isolated from a genetically manipulated source
Details: COMPLEXED WITH PK-MCO, AN ANALOGUE OF GB3 (GLOBOTRIAOSYL CERAMIDE)
Source: (gene. exp.) Phage h30, Enterobacteria phage H-19B / Genus: , Lambda-like viruses / Species: , / Strain: , / 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.: 33
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: Polysaccharide
alpha-D-galactopyranose-(1-4)-beta-D-galactopyranose


Type: oligosaccharide / Mass: 342.297 Da / Num. of mol.: 16
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGalpa1-4DGalpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2112h-1b_1-5][a2112h-1a_1-5]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
[][b-D-Galp]{[(4+1)][a-D-Galp]{}}LINUCSPDB-CARE
#4: Sugar
ChemComp-GAL / beta-D-galactopyranose / beta-D-galactose / D-galactose / galactose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 11
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGalpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-galactopyranoseCOMMON NAMEGMML 1.0
b-D-GalpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GalSNFG CARBOHYDRATE SYMBOLGMML 1.0
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 345 / 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 / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.9 Å3/Da / Density % sol: 60 %
Description: ALTHOUGH THE HIGH RESOLUTION DATA HAVE VERY POOR STATISTICS, A STATISTICAL ANALYSIS PRESENTED IN THE STRUCTURE REPORT INDICATED USEFUL INFORMATION TO 2.8 ANGSTROMS RESOLUTION
Crystal growpH: 6 / Details: pH 6.0
Crystal grow
*PLUS
Method: unknown

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Data collection

DiffractionMean temperature: 287 K
Diffraction sourceSource: ROTATING ANODE / Type: MACSCIENCE M18X / Wavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: Jul 1, 1994
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.8→21 Å / Num. obs: 41759 / % possible obs: 81.6 % / Observed criterion σ(I): 0 / Redundancy: 2.7 % / Rmerge(I) obs: 0.176 / Rsym value: 0.176 / Net I/σ(I): 3.37
Reflection shellResolution: 2.8→2.98 Å / Redundancy: 1.75 % / Rmerge(I) obs: 0.476 / Mean I/σ(I) obs: 0.581 / Rsym value: 0.476 / % possible all: 57.3
Reflection
*PLUS
Num. measured all: 113473
Reflection shell
*PLUS
% possible obs: 57.3 %

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Processing

Software
NameVersionClassification
XENGENdata collection
XENGENdata reduction
X-PLOR3.8model building
X-PLOR3.8refinement
XENGENdata scaling
X-PLOR3.8phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1BOV

1bov
PDB Unreleased entry


Resolution: 2.8→21 Å / Data cutoff high absF: 10000000 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: CROSS-VALIDATION DATA ARE LIKELY TO BE SOMEWHAT OVER-FIT BECAUSE OF THE HIGH DEGREE OF NCS. CARBOHYDRATE PARAMETER AND TOPOLOGY FILES PARAM3.CHO AND TOPH3_MOD.CHO WERE OBTAINED FROM BILL WEIS.
RfactorNum. reflection% reflectionSelection details
Rfree0.226 2078 5 %RANDOM
Rwork0.17 ---
obs0.17 41579 81.6 %-
Refinement stepCycle: LAST / Resolution: 2.8→21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10800 0 1622 345 12767
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.015
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg2.6
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d25
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.01
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.470.25
X-RAY DIFFRACTIONx_mcangle_it2.77
X-RAY DIFFRACTIONx_scbond_it3.470.5
X-RAY DIFFRACTIONx_scangle_it5.72
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Weight Biso : 1

Ens-IDDom-IDNCS model detailsRms dev Biso (Å2)Rms dev position (Å)Weight position
11RESTRAINTS4.910.06200
227.390.1510
334.810.255
LS refinement shellResolution: 2.8→2.9 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.36 123 5.3 %
Rwork0.288 2337 -
obs--49 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARAM19X.PROTOPH19X.PRO
X-RAY DIFFRACTION2PARAM19.SOLTOPH19.SOL
X-RAY DIFFRACTION3PARAM3.CHOTOPH3_MOD.CHO
Software
*PLUS
Name: X-PLOR / Version: 3.8 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg25
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.01
LS refinement shell
*PLUS
Rfactor obs: 0.288

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