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- PDB-1qnu: Shiga-Like Toxin I B Subunit Complexed with the Bridged-Starfish ... -

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Basic information

Entry
Database: PDB / ID: 1qnu
TitleShiga-Like Toxin I B Subunit Complexed with the Bridged-Starfish Inhibitor
ComponentsShiga toxin 1 variant B subunit
KeywordsTOXIN / SUBNANOMOLAR INHIBITOR / MULTIVALENT 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
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
METHYL-CARBAMIC ACID ETHYL ESTER / ETHYL-CARBAMIC ACID METHYL ESTER / Shiga toxin subunit B / Shiga toxin I subunit B
Similarity search - Component
Biological speciesEscherichia coli O157:H7 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.23 Å
AuthorsPannu, N.S. / Hayakawa, K. / Read, R.J.
Citation
Journal: Nature / Year: 2000
Title: Shiga-like toxins are neutralized by tailored multivalent carbohydrate ligands.
Authors: Kitov, P.I. / Sadowska, J.M. / Mulvey, G. / Armstrong, G.D. / Ling, H. / Pannu, N.S. / Read, R.J. / Bundle, D.R.
#1: Journal: Biochemistry / Year: 1998
Title: Structure of the Shiga-Like Toxin I B-Pentamer Complexed with an Analogue of its Receptor Bg3
Authors: Ling, H. / Boodhoo, A. / Hazes, B. / Cummings, M.D. / Armstrong, G.D. / Brunton, J.L. / Read, R.J.
History
DepositionOct 21, 1999Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 11, 2000Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 30, 2018Group: Data collection / Structure summary / Category: struct / Item: _struct.title
Revision 1.4Jun 13, 2018Group: Data collection / Database references ...Data collection / Database references / Source and taxonomy / Structure summary
Category: citation / entity ...citation / entity / entity_src_gen / struct_ref / struct_ref_seq
Item: _citation.page_last / _citation.title ..._citation.page_last / _citation.title / _entity.pdbx_description / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name / _entity_src_gen.pdbx_seq_type / _struct_ref.db_code / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.pdbx_db_accession
Revision 1.5May 8, 2019Group: Data collection / Derived calculations / Experimental preparation
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / struct_conn
Item: _exptl_crystal_grow.method / _struct_conn.pdbx_leaving_atom_flag
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / 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 / pdbx_validate_chiral / pdbx_validate_close_contact / 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 / _pdbx_database_status.status_code_sf / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_chiral.auth_asym_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_seq_id_1 / _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.ptnr1_symmetry / _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_conn.ptnr2_symmetry
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 2.2Nov 6, 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: Shiga toxin 1 variant B subunit
B: Shiga toxin 1 variant B subunit
C: Shiga toxin 1 variant B subunit
D: Shiga toxin 1 variant B subunit
E: Shiga toxin 1 variant B subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,04720
Polymers38,4935
Non-polymers3,55315
Water1,44180
1
A: Shiga toxin 1 variant B subunit
B: Shiga toxin 1 variant B subunit
C: Shiga toxin 1 variant B subunit
D: Shiga toxin 1 variant B subunit
E: Shiga toxin 1 variant B subunit
hetero molecules

A: Shiga toxin 1 variant B subunit
B: Shiga toxin 1 variant B subunit
C: Shiga toxin 1 variant B subunit
D: Shiga toxin 1 variant B subunit
E: Shiga toxin 1 variant B subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,09340
Polymers76,98610
Non-polymers7,10730
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area17830 Å2
ΔGint-84.1 kcal/mol
Surface area33650 Å2
MethodPQS
Unit cell
Length a, b, c (Å)104.470, 71.610, 56.360
Angle α, β, γ (deg.)90.00, 109.02, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.382759, 0.89895, -0.213035), (-0.898579, 0.308693, -0.311871), (0.214594, 0.310801, 0.925933)-0.018, 0.085, -0.013
2given(-0.616651, 0.553131, -0.560167), (-0.551662, -0.811247, -0.193769), (-0.561614, 0.189535, 0.805398)0.06, 0.101, 0.063
3given(-0.612174, -0.555757, -0.562474), (0.557655, -0.807756, 0.19118), (-0.560592, -0.196631, 0.804408)0.078, 0.064, 0.114
4given(0.387512, -0.896514, -0.214701), (0.896586, 0.312356, 0.313953), (-0.2144, -0.314159, 0.924844)0.009, -0.068, 0.081
DetailsBIOLOGICAL_UNIT: PENTAMER

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Components

#1: Protein
Shiga toxin 1 variant B subunit / VEROTOXIN I B SUBUNIT


Mass: 7698.634 Da / Num. of mol.: 5 / Fragment: RECEPTOR-BINDING DOMAIN
Source method: isolated from a genetically manipulated source
Details: COMPLEXED WITH BRIDGE-STARFISH MOLECULE, A SUBNANOMOLAR TAILORED MULTIVALENT INHIBITOR
Source: (gene. exp.) Escherichia coli O157:H7 (bacteria) / Gene: stx1 / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q7WZI6, UniProt: V5URS0*PLUS
#2: Polysaccharide
beta-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
DGalpb1-4DGalpb1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1a_1-5][a2112h-1b_1-5]/1-2-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][b-D-Galp]{[(4+1)][a-D-Galp]{}}}LINUCSPDB-CARE
#3: Chemical
ChemComp-EMB / METHYL-CARBAMIC ACID ETHYL ESTER


Mass: 103.120 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C4H9NO2
#4: Chemical
ChemComp-MEC / ETHYL-CARBAMIC ACID METHYL ESTER


Mass: 103.120 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C4H9NO2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 80 / 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: 2.39 Å3/Da / Density % sol: 49 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 7
Details: COMPLEX PREPARED BY ADDING 15 MICROLITRES OF BRIDGE-STARFIS (0.35MM) SLOWLY TO 15 MICROLITRES OF SLT-I B-SUBUNIT (10 MG WHILE AGITATING. HANGING DROPS WERE PREPARED BY MIXING THI SOLUTION ...Details: COMPLEX PREPARED BY ADDING 15 MICROLITRES OF BRIDGE-STARFIS (0.35MM) SLOWLY TO 15 MICROLITRES OF SLT-I B-SUBUNIT (10 MG WHILE AGITATING. HANGING DROPS WERE PREPARED BY MIXING THI SOLUTION WITH AN EQUAL VOLUME OF RESERVOIR SOLUTION (28% SA NH4SO4, 2% 2-METHYL-2,4-PENTANEDIOL, 0.1M NACL, 0.1 M HEPES, pH 7.00
Crystal grow
*PLUS
pH: 8 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlprotein1drop
20.1 M1dropNaCl
310 mMTris-HCl1drop
428 %satammonium sulfate1reservoir
52 %MPD1reservoir
60.1 M1reservoirNaCl
70.1 MHEPES1reservoir

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Data collection

DiffractionMean temperature: 287 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU/MSC RU- / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 15, 1999 / Details: YALE MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.23→50 Å / Num. obs: 19159 / % possible obs: 99 % / Observed criterion σ(I): 0 / Redundancy: 5.3 % / Biso Wilson estimate: 12.8 Å2 / Rmerge(I) obs: 0.148 / Rsym value: 0.148 / Net I/σ(I): 3.4
Reflection shellResolution: 2.23→2.35 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.291 / Mean I/σ(I) obs: 2.1 / Rsym value: 0.291 / % possible all: 96.2
Reflection
*PLUS
Rmerge(I) obs: 0.161
Reflection shell
*PLUS
Lowest resolution: 2.34 Å / % possible obs: 94.9 % / Rmerge(I) obs: 0.339

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Processing

Software
NameVersionClassification
CNS0.5refinement
MOSFLMdata reduction
SCALAdata scaling
CNS0.5phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1BOS

1bos


Resolution: 2.23→50 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1625101.21 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.184 1064 5.6 %SHELLS
Rwork0.171 ---
obs0.171 19150 99.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 51.4401 Å2 / ksol: 0.411496 e/Å3
Displacement parametersBiso mean: 26.3 Å2
Baniso -1Baniso -2Baniso -3
1-1.2 Å20 Å22.85 Å2
2--5 Å20 Å2
3----6.19 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.22 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.17 Å0.17 Å
Refinement stepCycle: LAST / Resolution: 2.23→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2700 0 240 80 3020
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.7
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.081.5
X-RAY DIFFRACTIONc_mcangle_it1.662
X-RAY DIFFRACTIONc_scbond_it2.052
X-RAY DIFFRACTIONc_scangle_it3.182.5
Refine LS restraints NCSRms dev Biso : 4.81 Å2 / Rms dev position: 0.25 Å / Weight Biso : 1 / Weight position: 5
LS refinement shellResolution: 2.23→2.37 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.212 141 4.5 %
Rwork0.202 2968 -
obs--97.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2STARFISH.PARSTARFISH.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER_REP.TOP
Software
*PLUS
Name: CNS / Version: 0.5 / Classification: refinement
Refinement
*PLUS
σ(F): 0
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg25
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.7

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