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- PDB-2bos: A MUTANT SHIGA-LIKE TOXIN IIE BOUND TO ITS RECEPTOR -

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Basic information

Entry
Database: PDB / ID: 2bos
TitleA MUTANT SHIGA-LIKE TOXIN IIE BOUND TO ITS RECEPTOR
ComponentsPROTEIN (SHIGA-LIKE TOXIN IIE B SUBUNIT)
KeywordsTOXIN / RECEPTOR BINDING / PROTEIN-CARBOHYDRATE RECOGNITION / SPECIFICITY
Function / homology
Function and homology information


symbiont-mediated hemolysis of host erythrocyte / 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
N-BUTANE / : / Orf protein
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsLing, H. / Boodhoo, A. / Armstrong, G.D. / Clark, C.G. / Brunton, J.L. / Read, R.J.
Citation
Journal: Structure Fold.Des. / Year: 2000
Title: A mutant Shiga-like toxin IIe bound to its receptor Gb(3): structure of a group II Shiga-like toxin with altered binding specificity.
Authors: Ling, H. / Pannu, N.S. / Boodhoo, A. / Armstrong, G.D. / Clark, C.G. / Brunton, J.L. / Read, R.J.
#1: 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.
#2: 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
DepositionOct 20, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Oct 20, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / 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 / 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 / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_seq_id / _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
Revision 2.2Aug 23, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 2.3Oct 16, 2024Group: Structure summary / Category: 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: PROTEIN (SHIGA-LIKE TOXIN IIE B SUBUNIT)
B: PROTEIN (SHIGA-LIKE TOXIN IIE B SUBUNIT)
C: PROTEIN (SHIGA-LIKE TOXIN IIE B SUBUNIT)
D: PROTEIN (SHIGA-LIKE TOXIN IIE B SUBUNIT)
E: PROTEIN (SHIGA-LIKE TOXIN IIE B SUBUNIT)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,33315
Polymers37,9525
Non-polymers3,38110
Water2,882160
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11200 Å2
ΔGint25 kcal/mol
Surface area14240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.077, 78.618, 78.468
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
/ NCS ensembles :
ID
1
2

NCS oper:
IDCodeMatrixVector
1given(0.386135, -0.51221, 0.767164), (0.785488, 0.618624, 0.017677), (-0.48364, 0.595773, 0.641207)-4.906, -20.241, 22.559
2given(-0.621021, -0.013133, 0.783683), (0.783763, -0.001598, 0.621058), (-0.006904, 0.999912, 0.011286)20.16, -36.399, 27.197
3given(-0.606833, 0.794812, -0.005215), (0.033614, 0.032218, 0.998915), (0.794118, 0.606, -0.046268)40.715, -28.164, 8.358
4given(0.388573, 0.806276, -0.446015), (-0.465945, 0.589542, 0.659799), (0.794925, -0.048561, 0.604761)27.385, -5.372, -8.94

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Components

#1: Protein
PROTEIN (SHIGA-LIKE TOXIN IIE B SUBUNIT) / VEROCYTOTOXIN


Mass: 7590.411 Da / Num. of mol.: 5 / Fragment: RECEPTOR-BINDING DOMAIN / Mutation: Q65E, K67Q
Source method: isolated from a genetically manipulated source
Details: COMPLEXED WITH PK-MCO, AN ANALOGUE OF GB3 (GLOBOTRIAOSYL CERAMIDE)
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: PIR: B32360, UniProt: Q47644*PLUS
#2: Polysaccharide
alpha-D-galactopyranose-(1-4)-beta-D-galactopyranose-(1-4)-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 504.438 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGalpa1-4DGalpb1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,3,2/[a2122h-1a_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.: 2
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: Chemical ChemComp-NBU / N-BUTANE


Mass: 58.122 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 160 / 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: 2.38 Å3/Da / Density % sol: 51.23 %
Crystal growpH: 8.4
Details: PROTEIN WAS CRYSTALLIZED FROM 1 M NACL,10 MM TRIS-HCL BUFFE, pH 8.4
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Details: drop consists of equal volume of protein and reservoir solutions
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
15 mg/mlprotein1drop
21 M1reservoirNaCl
310 mMTris-HCl1reservoir

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Data collection

DiffractionMean temperature: 287 K
Diffraction sourceSource: ROTATING ANODE / Type: SIEMENS / Wavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: Nov 15, 1994
RadiationMonochromator: GRAPHITE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→31 Å / Num. obs: 25704 / % possible obs: 95.3 % / Observed criterion σ(I): 0 / Redundancy: 12 % / Rmerge(I) obs: 0.082 / Rsym value: 0.082 / Net I/σ(I): 13.5
Reflection shellResolution: 2→2.03 Å / Rmerge(I) obs: 0.216 / Mean I/σ(I) obs: 1.66 / Rsym value: 0.216 / % possible all: 82.4
Reflection
*PLUS
Num. measured all: 308496 / Rmerge(I) obs: 0.102
Reflection shell
*PLUS
Lowest resolution: 2.15 Å / % possible obs: 87.2 % / Rmerge(I) obs: 0.222

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Processing

Software
NameVersionClassification
X-GENdata scaling
X-GENdata reduction
AMoREphasing
BRUTEmodel building
X-PLOR3.8refinement
BRUTEphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1BOV

1bov
PDB Unreleased entry


Resolution: 2→31 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 5-FOLD NCS.
RfactorNum. reflection% reflectionSelection details
Rfree0.194 2571 10 %RANDOM
Rwork0.155 ---
obs0.155 25704 95.3 %-
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-6.15 Å20 Å20 Å2
2--4.14 Å20 Å2
3---5.83 Å2
Refinement stepCycle: LAST / Resolution: 2→31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2690 0 228 160 3078
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_deg1.6
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.4
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.4
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.0890.25
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it3.1830.5
X-RAY DIFFRACTIONx_scangle_it
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Weight Biso : 3.5

Ens-IDDom-IDNCS model detailsRms dev Biso (Å2)Rms dev position (Å)Weight position
11RESTRAINTS3.020.210.043
223.1550.15310.21
LS refinement shellResolution: 2→2.03 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.251 64 7.7 %
Rwork0.198 64 -
obs--82.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM3.CHOTOPH3.CHO
X-RAY DIFFRACTION3PARAM19.SOLTOPH19.SOL
Software
*PLUS
Name: X-PLOR / Version: 3.8 / Classification: refinement
Refinement
*PLUS
Num. reflection Rfree: 2541
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.4
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.4

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