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- PDB-2xsc: Crystal structure of the cell-binding B oligomer of verotoxin-1 f... -

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Basic information

Entry
Database: PDB / ID: 2xsc
TitleCrystal structure of the cell-binding B oligomer of verotoxin-1 from E. coli
ComponentsSHIGA-LIKE TOXIN 1 SUBUNIT B
KeywordsTOXIN
Function / homology
Function and homology information


symbiont-mediated modulation of host virulence / 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 / MIR / Resolution: 2.052 Å
AuthorsStein, P.E. / Boodhoo, A. / Tyrrell, G.J. / Brunton, J.L. / Oeffner, R.D. / Bunkoczi, G. / Read, R.J.
CitationJournal: 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
DepositionSep 27, 2010Deposition site: PDBE / Processing site: PDBE
SupersessionOct 13, 2010ID: 1BOV
Revision 1.0Oct 13, 2010Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_label_seq_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_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SHIGA-LIKE TOXIN 1 SUBUNIT B
B: SHIGA-LIKE TOXIN 1 SUBUNIT B
C: SHIGA-LIKE TOXIN 1 SUBUNIT B
D: SHIGA-LIKE TOXIN 1 SUBUNIT B
E: SHIGA-LIKE TOXIN 1 SUBUNIT B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,6898
Polymers38,4935
Non-polymers1963
Water2,612145
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6210 Å2
ΔGint-39.5 kcal/mol
Surface area14340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.600, 102.400, 56.100
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
21
31
41
51
12
22
32
42
52
13
23
33
43
53

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN D AND BACKBONE AND NOT (ELEMENT H OR ELEMENT...
211CHAIN A AND BACKBONE AND NOT (ELEMENT H OR ELEMENT...
311CHAIN C AND BACKBONE AND NOT (ELEMENT H OR ELEMENT...
411CHAIN E AND BACKBONE AND NOT (ELEMENT H OR ELEMENT...
511CHAIN B AND BACKBONE AND NOT (ELEMENT H OR ELEMENT...
112CHAIN D AND BACKBONE AND NOT (ELEMENT H OR ELEMENT...
212CHAIN A AND BACKBONE AND NOT (ELEMENT H OR ELEMENT...
312CHAIN C AND BACKBONE AND NOT (ELEMENT H OR ELEMENT...
412CHAIN E AND BACKBONE AND NOT (ELEMENT H OR ELEMENT...
512CHAIN B AND BACKBONE AND NOT (ELEMENT H OR ELEMENT...
113CHAIN D AND SIDECHAIN AND NOT (ELEMENT H OR ELEMENT...
213CHAIN A AND SIDECHAIN AND NOT (ELEMENT H OR ELEMENT...
313CHAIN C AND SIDECHAIN AND NOT (ELEMENT H OR ELEMENT...
413CHAIN E AND SIDECHAIN AND NOT (ELEMENT H OR ELEMENT...
513CHAIN B AND SIDECHAIN AND NOT (ELEMENT H OR ELEMENT...

NCS ensembles :
ID
1
2
3

NCS oper:
IDCodeMatrixVector
1given(0.66772, 0.74199, -0.05993), (-0.50405, 0.39141, -0.76989), (-0.54779, 0.54428, 0.63536)-7.67502, 14.74852, -11.4853
2given(0.09731, 0.69728, -0.71016), (-0.15327, -0.69454, -0.70294), (-0.98338, 0.17725, 0.03928)-6.16588, 32.57329, -2.07367
3given(0.08401, -0.07394, -0.99372), (0.63323, -0.76603, 0.11053), (-0.76939, -0.63853, -0.01754)6.47485, 30.19076, 12.07049
4given(0.62561, -0.53374, -0.56898), (0.77047, 0.30828, 0.55798), (-0.12241, -0.78745, 0.60409)11.54872, 9.70221, 13.46176

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Components

#1: Protein
SHIGA-LIKE TOXIN 1 SUBUNIT B / SLT-1 B SUBUNIT / SLT-1B / SLT-IB / VEROCYTOTOXIN 1 SUBUNIT B / VEROTOXIN 1 SUBUNIT B


Mass: 7698.634 Da / Num. of mol.: 5 / Fragment: RESIDUES 21-89 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: TB1 (PJLB 120) / References: UniProt: P69178, UniProt: P69179*PLUS
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 145 / 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: 2.23 Å3/Da / Density % sol: 45 % / Description: NONE
Crystal growpH: 7 / Details: 12% PEG8000, 50 MM MOPS PH7.0

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Data collection

DiffractionMean temperature: 287 K
Diffraction sourceSource: ROTATING ANODE / Wavelength: 1.5418
DetectorType: MULTIWIRE / Detector: AREA DETECTOR
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.05→24.6 Å / Num. obs: 19617 / % possible obs: 88.6 % / Observed criterion σ(I): 0 / Biso Wilson estimate: 21.59 Å2

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MLPHAREphasing
RefinementMethod to determine structure: MIR
Starting model: NONE

Resolution: 2.052→24.634 Å / SU ML: 0.19 / σ(F): 0.03 / Phase error: 20.17 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1917 1005 5.1 %
Rwork0.1423 --
obs0.1448 19617 88.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 20.811 Å2 / ksol: 0.34 e/Å3
Displacement parametersBiso mean: 23.3 Å2
Baniso -1Baniso -2Baniso -3
1--2.7744 Å2-0 Å20 Å2
2---2.4198 Å20 Å2
3---5.1942 Å2
Refinement stepCycle: LAST / Resolution: 2.052→24.634 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2700 0 3 145 2848
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.015460
X-RAY DIFFRACTIONf_angle_d0.9489798
X-RAY DIFFRACTIONf_dihedral_angle_d13.71361
X-RAY DIFFRACTIONf_chiral_restr0.073445
X-RAY DIFFRACTIONf_plane_restr0.004856
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11D168X-RAY DIFFRACTIONPOSITIONAL
12A168X-RAY DIFFRACTIONPOSITIONAL0.14
13C168X-RAY DIFFRACTIONPOSITIONAL0.132
14E168X-RAY DIFFRACTIONPOSITIONAL0.126
15B136X-RAY DIFFRACTIONPOSITIONAL0.148
21D84X-RAY DIFFRACTIONPOSITIONAL
22A84X-RAY DIFFRACTIONPOSITIONAL0.287
23C88X-RAY DIFFRACTIONPOSITIONAL0.226
24E88X-RAY DIFFRACTIONPOSITIONAL0.239
25B52X-RAY DIFFRACTIONPOSITIONAL0.261
31D216X-RAY DIFFRACTIONPOSITIONAL
32A216X-RAY DIFFRACTIONPOSITIONAL0.347
33C227X-RAY DIFFRACTIONPOSITIONAL0.298
34E227X-RAY DIFFRACTIONPOSITIONAL0.27
35B157X-RAY DIFFRACTIONPOSITIONAL0.31
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0525-2.16060.24851120.20271386X-RAY DIFFRACTION48
2.1606-2.29590.23941200.17062560X-RAY DIFFRACTION86
2.2959-2.4730.2125970.15272759X-RAY DIFFRACTION92
2.473-2.72160.23651910.15022789X-RAY DIFFRACTION95
2.7216-3.11480.1911480.13342955X-RAY DIFFRACTION99
3.1148-3.92170.16511720.11872999X-RAY DIFFRACTION100
3.9217-24.63610.15831650.12693164X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.5546-0.0753-0.01560.7632-0.62011.420.127-0.05980.0561-0.08720.10030.111-0.107-0.0448-0.10730.1292-0.0048-0.01110.14730.00590.06974.242224.898-24.406
21.30130.44380.75141.1885-0.55541.423-0.07950.20210.3916-0.15940.02870.2246-0.0707-0.20920.0270.1236-0.01180.00130.14730.01390.201715.198641.0237-15.6692
31.0819-0.1047-0.08020.62850.03830.3656-0.0450.10320.1886-0.07740.0397-0.0951-0.0528-0.0364-0.00490.0615-0.01860.00380.07210.00330.059629.008731.6205-2.9688
41.049-0.4320.30670.80111.32751.0225-0.0128-0.0381-0.10510.0740.12660.05270.18370.0185-0.09320.09040.00170.01380.03490.03050.07229.122610.9712-6.7722
52.4395-1.27330.3743-0.4250.02451.09260.12580.2101-0.8352-0.1244-0.03330.26820.3495-0.0713-0.12320.2048-0.0433-0.0620.1093-0.03330.271214.78887.231-21.4882
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A
2X-RAY DIFFRACTION2CHAIN B
3X-RAY DIFFRACTION3CHAIN C
4X-RAY DIFFRACTION4CHAIN D
5X-RAY DIFFRACTION5CHAIN E

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