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- PDB-1c4q: MUTATED SHIGA-LIKE TOXIN B SUBUNIT (F30A/W34A) COMPLEXED WITH REC... -

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Basic information

Entry
Database: PDB / ID: 1c4q
TitleMUTATED SHIGA-LIKE TOXIN B SUBUNIT (F30A/W34A) COMPLEXED WITH RECEPTOR GB3 ANALOGUE
ComponentsPROTEIN (SHIGA-LIKE TOXIN I SUBUNIT B)
KeywordsTOXIN / RECEPTOR BINDING / PROTEIN-CARBOHYDRATE RECOGNITION / OB-FOLD
Function / homology
Function and homology information


modulation of host virulence by virus / 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 / MOLECULAR REPLACEMENT / Resolution: 1.52 Å
AuthorsLing, H. / Brunton, J.L. / Read, R.J.
Citation
Journal: To be Published
Title: Identification of the Primary Receptor Binding Site of Shiga-Like Toxin B Subunits: Structures of Mutated Shiga-Like Toxin I B-Pentamer with and without Bound Carbohydrate
Authors: Ling, H. / Bast, D. / 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. / La Boodhoo, J. / Hazes, B. / Cummings, M.D. / Armstrong, G.D. / Brunton, J.L. / Read, R.J.
History
DepositionAug 31, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 20, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.source
Revision 1.5Mar 14, 2018Group: Database references / Category: struct_ref_seq_dif / Item: _struct_ref_seq_dif.details
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / 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_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 / _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
Revision 2.1Aug 9, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTEIN (SHIGA-LIKE TOXIN I SUBUNIT B)
B: PROTEIN (SHIGA-LIKE TOXIN I SUBUNIT B)
C: PROTEIN (SHIGA-LIKE TOXIN I SUBUNIT B)
D: PROTEIN (SHIGA-LIKE TOXIN I SUBUNIT B)
E: PROTEIN (SHIGA-LIKE TOXIN I SUBUNIT B)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,05910
Polymers37,5375
Non-polymers2,5225
Water7,008389
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10890 Å2
ΔGint10 kcal/mol
Surface area13450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.269, 44.165, 54.007
Angle α, β, γ (deg.)106.24, 106.69, 98.87
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.339709, -0.926657, -0.160949), (0.931875, 0.308455, 0.190956), (-0.127306, -0.214854, 0.968314)29.116, -39.9257, 4.8519
2given(-0.663922, -0.59307, -0.455496), (0.615463, -0.779338, 0.117636), (-0.424751, -0.20224, 0.882432)73.4746, -26.8361, 18.2715
3given(-0.643159, 0.561526, -0.520611), (-0.582412, -0.800127, -0.143503), (-0.497135, 0.210914, 0.841648)72.8158, 25.0657, 20.7311
4given(0.329328, 0.936505, -0.120421), (-0.930738, 0.300504, -0.208384), (-0.158966, 0.180707, 0.970605)28.1841, 40.248, 7.868

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Components

#1: Protein
PROTEIN (SHIGA-LIKE TOXIN I SUBUNIT B)


Mass: 7507.405 Da / Num. of mol.: 5 / Fragment: RECEPTOR-BINDING DOMAIN / Mutation: F30A, W34A
Source method: isolated from a genetically manipulated source
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.: 5
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 / Water


Mass: 18.015 Da / Num. of mol.: 389 / 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: 50.82 %
Crystal growpH: 7.5 / Details: pH 7.5

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: SIEMENS / Wavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: May 1, 1998
RadiationMonochromator: GRAPHITE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.52→38.7 Å / Num. obs: 54074 / % possible obs: 96.7 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.056 / Rsym value: 0.056
Reflection shellHighest resolution: 1.52 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.287 / Rsym value: 0.287 / % possible all: 82.7

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Processing

Software
NameVersionClassification
X-GENdata scaling
X-GENdata reduction
AMoREphasing
CNS0.3Drefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1BOS

1bos


Resolution: 1.52→38.7 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.194 1164 2.1 %THIN SHELLS
Rwork0.17 ---
obs0.17 54074 96.7 %-
Solvent computationBsol: 30.5 Å2 / ksol: 0.334 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.034 Å20.906 Å23.008 Å2
2---1.173 Å22.035 Å2
3---0.139 Å2
Refinement stepCycle: LAST / Resolution: 1.52→38.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2673 0 170 389 3232
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.02
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_deg1.9
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it0.8321.5
X-RAY DIFFRACTIONc_mcangle_it1.3452
X-RAY DIFFRACTIONc_scbond_it1.3062
X-RAY DIFFRACTIONc_scangle_it2.0522.5
Refine LS restraints NCSNCS model details: RESTRAINTS
LS refinement shellResolution: 1.52→1.54 Å / Total num. of bins used: 23
RfactorNum. reflection% reflection
Rfree0.319 241 1.3 %
Rwork0.301 1771 -
obs--82.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM19.SOLTOPH3.CHO
X-RAY DIFFRACTION3PARAM3.CHOTOPH19.SOL

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