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- PDB-1qoh: A MUTANT SHIGA-LIKE TOXIN IIE -

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Basic information

Entry
Database: PDB / ID: 1qoh
TitleA MUTANT SHIGA-LIKE TOXIN IIE
ComponentsSHIGA-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
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsPannu, N.S. / Boodhoo, A. / Armstrong, G.D. / Clark, C.G. / Brunton, J.L. / Read, R.J.
Citation
Journal: Structure / 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
DepositionNov 8, 1999Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 3, 2000Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)151,80820
Polymers151,80820
Non-polymers00
Water6,467359
1
A: SHIGA-LIKE TOXIN IIE B SUBUNIT
B: SHIGA-LIKE TOXIN IIE B SUBUNIT
C: SHIGA-LIKE TOXIN IIE B SUBUNIT
D: SHIGA-LIKE TOXIN IIE B SUBUNIT
E: SHIGA-LIKE TOXIN IIE B SUBUNIT


Theoretical massNumber of molelcules
Total (without water)37,9525
Polymers37,9525
Non-polymers00
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
F: SHIGA-LIKE TOXIN IIE B SUBUNIT
G: SHIGA-LIKE TOXIN IIE B SUBUNIT
H: SHIGA-LIKE TOXIN IIE B SUBUNIT
I: SHIGA-LIKE TOXIN IIE B SUBUNIT
J: SHIGA-LIKE TOXIN IIE B SUBUNIT


Theoretical massNumber of molelcules
Total (without water)37,9525
Polymers37,9525
Non-polymers00
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
K: SHIGA-LIKE TOXIN IIE B SUBUNIT
L: SHIGA-LIKE TOXIN IIE B SUBUNIT
M: SHIGA-LIKE TOXIN IIE B SUBUNIT
N: SHIGA-LIKE TOXIN IIE B SUBUNIT
O: SHIGA-LIKE TOXIN IIE B SUBUNIT


Theoretical massNumber of molelcules
Total (without water)37,9525
Polymers37,9525
Non-polymers00
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
4
P: SHIGA-LIKE TOXIN IIE B SUBUNIT
Q: SHIGA-LIKE TOXIN IIE B SUBUNIT
R: SHIGA-LIKE TOXIN IIE B SUBUNIT
S: SHIGA-LIKE TOXIN IIE B SUBUNIT
T: SHIGA-LIKE TOXIN IIE B SUBUNIT


Theoretical massNumber of molelcules
Total (without water)37,9525
Polymers37,9525
Non-polymers00
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)113.490, 54.510, 116.890
Angle α, β, γ (deg.)90.00, 109.12, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.891855, -0.143341, -0.429008), (-0.356383, 0.361382, -0.861623), (0.278542, 0.921334, 0.271216)21.95, 44.642, 38.372
2given(0.69855, -0.5378, -0.472015), (-0.714894, -0.552994, -0.42793), (-0.030881, 0.636372, -0.770764)24.809, 21.256, 90.41
3given(0.694573, -0.718995, 0.024766), (-0.549575, -0.508064, 0.663203), (-0.464257, -0.474254, -0.74803)-1.544, -34.976, 88.495
4given(0.892932, -0.347393, 0.286339), (-0.119153, 0.430988, 0.894456), (-0.434137, -0.832807, 0.34345)-14.6, -46.137, 32.788
5given(-0.997623, -0.062974, 0.027978), (0.065356, -0.993381, 0.094461), (0.021845, 0.096065, 0.995135)-2.213, 3.775, 55.151
6given(-0.8466, 0.135203, 0.514771), (0.460131, -0.300157, 0.835574), (0.267484, 0.944259, 0.191902)-27.383, -34.162, 97.2
7given(-0.655464, 0.592168, 0.468726), (0.752334, 0.566246, 0.336688), (-0.066038, 0.573325, -0.816662)-24.839, -8.106, 147.526
8given(-0.66695, 0.739868, -0.088163), (0.551943, 0.411093, -0.725507), (-0.500537, -0.532538, -0.682544)4.378, 46.847, 139.91299
9given(-0.889526, 0.309404, -0.336174), (0.136309, -0.522566, -0.841632), (-0.436077, -0.794477, 0.422662)16.559, 52.059, 83.639
10given(0.716742, -0.34381, -0.606692), (-0.489311, 0.371915, -0.788831), (0.496846, 0.862249, 0.098337)51.344, 43.938, -2.906
11given(0.603996, -0.773219, -0.193185), (-0.775711, -0.514706, -0.36517), (0.182923, 0.370417, -0.910675)29.323, 22.183, 48.716
12given(0.782555, -0.55553, 0.281057), (-0.580003, -0.486442, 0.65343), (-0.226282, -0.674359, -0.702877)5.677, -29.525, 37.138
13given(0.693999, -0.71954, 0.02506), (-0.549709, -0.507075, 0.663848), (-0.464958, -0.474486, -0.747447)-1.563, -35.022, 88.448
14given(0.934071, 0.063263, -0.351439), (-0.082625, 0.995763, -0.040356), (0.347397, 0.066732, 0.93534)39.374, 6.572, -46.015
15given(-0.969898, 0.100379, -0.221861), (0.137855, -0.5247, -0.840051), (-0.200734, -0.845348, 0.495068)29.45, 48.705, 30.126
16given(-0.93002, -0.045826, 0.364639), (0.076547, -0.994589, 0.07024), (0.359447, 0.093237, 0.928496)-2.3, 2.579, 9.678
17given(-0.739657, 0.379334, 0.555889), (0.457691, -0.322027, 0.828745), (0.493383, 0.867412, 0.064572)-10.804, -36.122, 53.991
18given(-0.649727, 0.737201, 0.185443), (0.745075, 0.569219, 0.347638), (0.150721, 0.364039, -0.919108)8.614, -11.221, 103.965
19given(-0.804043, 0.545985, -0.235405), (0.530476, 0.479929, -0.698758), (-0.268534, -0.686708, -0.675515)29.587, 42.121, 90.731
20given(0.891855, -0.143341, -0.429008), (-0.356383, 0.361382, -0.861623), (0.278542, 0.921334, 0.271216)21.95, 44.642, 38.372
DetailsTHERE ARE FOUR PENTAMERS PER ASYMMETRIC UNIT

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Components

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


Mass: 7590.411 Da / Num. of mol.: 20 / Fragment: RECEPTOR-BINDING DOMAIN / Mutation: YES
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: UniProt: Q47644
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 359 / 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: 2.25 Å3/Da / Density % sol: 45 %
Crystal growpH: 7.4
Details: 8% PEG8000, 0.1M NACL, 0.1M IMIDAZOLE, PH=7.4, pH 7.40
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
110 mg/mlprotein1drop
28 %PEG80001reservoir
30.1 M1reservoirNaCl
40.1 Mimidazole1reservoir

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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: Aug 15, 1993 / Details: COLLIMATOR
RadiationMonochromator: GRAPHITE(002) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.35→20.36 Å / Num. obs: 34188 / % possible obs: 60.1 % / Observed criterion σ(I): 0 / Redundancy: 1.83 % / Biso Wilson estimate: 41 Å2 / Rmerge(I) obs: 0.0844 / Rsym value: 0.0844 / Net I/σ(I): 8.415
Reflection shellResolution: 2.35→2.49 Å / Redundancy: 1.66 % / Rmerge(I) obs: 0.3296 / Mean I/σ(I) obs: 0.968 / Rsym value: 0.3296 / % possible all: 24.9
Reflection
*PLUS
Num. measured all: 62524
Reflection shell
*PLUS
% possible obs: 24.85 %

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Processing

Software
NameVersionClassification
CNS0.5refinement
XENGENdata reduction
XENGENdata scaling
CNS0.5phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1BOV AND 2BOS

1bov
PDB Unreleased entry

2bos


Resolution: 2.35→21 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 1888964.51 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.234 1055 3.1 %SHELLS
Rwork0.188 ---
obs0.188 34187 60.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 21.9572 Å2 / ksol: 0.296191 e/Å3
Displacement parametersBiso mean: 28.9 Å2
Baniso -1Baniso -2Baniso -3
1--2.87 Å20 Å24.49 Å2
2--4.65 Å20 Å2
3----1.78 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.36 Å0.33 Å
Luzzati d res low-5 Å
Luzzati sigma a0.48 Å0.42 Å
Refinement stepCycle: LAST / Resolution: 2.35→21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10660 0 0 359 11019
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.012
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_deg1.6
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.78
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.491.5
X-RAY DIFFRACTIONc_mcangle_it2.442
X-RAY DIFFRACTIONc_scbond_it2.412
X-RAY DIFFRACTIONc_scangle_it3.752.5
Refine LS restraints NCSRms dev Biso : 3.155 Å2 / Rms dev position: 0.153 Å / Weight Biso : 3.5 / Weight position: 0.21
LS refinement shellResolution: 2.35→2.5 Å / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree1 1 0 %
Rwork0.397 2567 -
obs--27.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
Software
*PLUS
Name: CNS / Version: 0.5 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.012
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.1
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.78

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