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- PDB-2xh6: Clostridium perfringens enterotoxin -

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Basic information

Entry
Database: PDB / ID: 2xh6
TitleClostridium perfringens enterotoxin
ComponentsHEAT-LABILE ENTEROTOXIN B CHAIN
KeywordsTOXIN / FOOD POISONING / ANTIBIOTIC-ASSOCIATED DIARRHOEA
Function / homology
Function and homology information


toxin activity / extracellular region
Similarity search - Function
Jelly Rolls - #1050 / Proaerolysin; Chain A, domain 3 - #20 / Proaerolysin; Chain A, domain 3 / Clostridium enterotoxin / Clostridium enterotoxin / Beta Complex / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
1,4-DIETHYLENE DIOXIDE / Heat-labile enterotoxin B chain
Similarity search - Component
Biological speciesCLOSTRIDIUM PERFRINGENS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.69 Å
AuthorsBriggs, D.C. / Naylor, C.E. / Smedley III, J.G. / MCClane, B.A. / Basak, A.K.
Citation
Journal: J.Mol.Biol. / Year: 2011
Title: Structure of the Food-Poisoning Clostridium Perfringens Enterotoxin Reveals Similarity to the Aerolysin-Like Pore-Forming Toxins
Authors: Briggs, D.C. / Naylor, C.E. / Smedley III, J.G. / Lukoyanova, N. / Robertson, S. / Mcclane, B.A. / Basak, A.K.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2010
Title: Crystallisation and Preliminary Crystallographic Analysis of the Clostridium Perfringens Enterotoxin.
Authors: Briggs, D.C. / Smedley III, J.G. / Mcclane, B.A. / Basak, A.K.
History
DepositionJun 9, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 27, 2011Provider: repository / Type: Initial release
Revision 1.1Aug 17, 2011Group: Database references / Refinement description / Version format compliance
Revision 1.2Oct 12, 2011Group: Database references
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Dec 20, 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

Downloads & links

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Assembly

Deposited unit
A: HEAT-LABILE ENTEROTOXIN B CHAIN
B: HEAT-LABILE ENTEROTOXIN B CHAIN
C: HEAT-LABILE ENTEROTOXIN B CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,8858
Polymers106,0363
Non-polymers8495
Water3,225179
1
A: HEAT-LABILE ENTEROTOXIN B CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,9025
Polymers35,3451
Non-polymers5574
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: HEAT-LABILE ENTEROTOXIN B CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,6382
Polymers35,3451
Non-polymers2921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: HEAT-LABILE ENTEROTOXIN B CHAIN


Theoretical massNumber of molelcules
Total (without water)35,3451
Polymers35,3451
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)210.664, 119.296, 74.834
Angle α, β, γ (deg.)90.00, 110.50, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
12
22
32
13
23
33

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN A AND (RESSEQ 35:63 OR RESSEQ 69:119 OR RESSEQ...
211CHAIN B AND (RESSEQ 35:63 OR RESSEQ 69:119 OR RESSEQ...
311CHAIN C AND (RESSEQ 35:63 OR RESSEQ 69:119 OR RESSEQ...
112CHAIN A AND (RESSEQ 187:222 ) AND (NOT ELEMENT H) AND (NOT ELEMENT D)
212CHAIN B AND (RESSEQ 187:222 ) AND (NOT ELEMENT H) AND (NOT ELEMENT D)
312CHAIN C AND (RESSEQ 187:222 ) AND (NOT ELEMENT H) AND (NOT ELEMENT D)
113CHAIN A AND (RESSEQ 223:272 OR RESSEQ 274:300 OR RESSEQ...
213CHAIN B AND (RESSEQ 223:272 OR RESSEQ 274:300 OR RESSEQ...
313CHAIN C AND (RESSEQ 223:272 OR RESSEQ 274:300 OR RESSEQ...

NCS ensembles :
ID
1
2
3

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Components

#1: Protein HEAT-LABILE ENTEROTOXIN B CHAIN / ENTEROTOXIN


Mass: 35345.207 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) CLOSTRIDIUM PERFRINGENS (bacteria) / Strain: NCTC8239 / References: UniProt: P01558
#2: Sugar ChemComp-BOG / octyl beta-D-glucopyranoside / Beta-Octylglucoside / octyl beta-D-glucoside / octyl D-glucoside / octyl glucoside


Type: D-saccharide / Mass: 292.369 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C14H28O6 / Comment: detergent*YM
IdentifierTypeProgram
b-octylglucosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Chemical ChemComp-DIO / 1,4-DIETHYLENE DIOXIDE


Mass: 88.105 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H8O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 179 / 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: 4.2 Å3/Da / Density % sol: 71 % / Description: NONE
Crystal growDetails: 32-40% V/V DIOXANE IN WATER

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9686
DetectorType: ADSC CCD / Detector: CCD / Date: Feb 21, 2003 / Details: MIRRORS
RadiationMonochromator: SILICON / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 2.7→70 Å / Num. obs: 42488 / % possible obs: 95.8 % / Observed criterion σ(I): 0 / Redundancy: 2.7 % / Biso Wilson estimate: 70.9 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 12
Reflection shellResolution: 2.68→2.82 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 2.2 / % possible all: 83.3

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 2QUO AND 2ZS6

2quo

2zs6


Resolution: 2.69→63.393 Å / SU ML: 0.49 / σ(F): 1.38 / Phase error: 24.34 / Stereochemistry target values: ML
Details: THERE IS A SLIGHT DISCREPANCY BETWEEN UNIQUE REFLECTIONS IN DATA COLLECTION AND REFINEMENT DUE TO THE USE OF SLIGHTLY DIFFERENT REFLECTION SELECTIONS IN EACH CASE, AND THE GENERATION OF A ...Details: THERE IS A SLIGHT DISCREPANCY BETWEEN UNIQUE REFLECTIONS IN DATA COLLECTION AND REFINEMENT DUE TO THE USE OF SLIGHTLY DIFFERENT REFLECTION SELECTIONS IN EACH CASE, AND THE GENERATION OF A COMPLETE REFLECTION SET FOR REFINEMENT.
RfactorNum. reflection% reflection
Rfree0.2492 2168 5.1 %
Rwork0.2112 --
obs0.2131 42676 88.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 36.654 Å2 / ksol: 0.331 e/Å3
Displacement parametersBiso mean: 55.7 Å2
Baniso -1Baniso -2Baniso -3
1-9.1143 Å2-0 Å23.0569 Å2
2---3.8889 Å20 Å2
3----5.2254 Å2
Refinement stepCycle: LAST / Resolution: 2.69→63.393 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6611 0 58 179 6848
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0146801
X-RAY DIFFRACTIONf_angle_d1.5329248
X-RAY DIFFRACTIONf_dihedral_angle_d17.1982410
X-RAY DIFFRACTIONf_chiral_restr0.1031058
X-RAY DIFFRACTIONf_plane_restr0.0061179
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A1070X-RAY DIFFRACTIONPOSITIONAL
12B1070X-RAY DIFFRACTIONPOSITIONAL0.131
13C1087X-RAY DIFFRACTIONPOSITIONAL0.153
21A264X-RAY DIFFRACTIONPOSITIONAL
22B264X-RAY DIFFRACTIONPOSITIONAL0.103
23C260X-RAY DIFFRACTIONPOSITIONAL0.1
31A762X-RAY DIFFRACTIONPOSITIONAL
32B762X-RAY DIFFRACTIONPOSITIONAL0.076
33C762X-RAY DIFFRACTIONPOSITIONAL0.073
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6889-2.7850.33552060.28733651X-RAY DIFFRACTION81
2.785-2.89650.30082100.25254191X-RAY DIFFRACTION91
2.8965-3.02830.30172070.23324158X-RAY DIFFRACTION91
3.0283-3.1880.28522240.22514153X-RAY DIFFRACTION91
3.188-3.38770.28622290.20914114X-RAY DIFFRACTION90
3.3877-3.64920.21832330.17464097X-RAY DIFFRACTION90
3.6492-4.01640.20972360.17574073X-RAY DIFFRACTION89
4.0164-4.59750.18511980.16584073X-RAY DIFFRACTION89
4.5975-5.79170.19722040.17424052X-RAY DIFFRACTION88
5.7917-63.41050.2482210.2063946X-RAY DIFFRACTION85
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)
10.41880.02550.39171.55581.09291.17450.10450.16830.0318-0.34140.1663-0.1671-0.05970.15380.01940.3643-0.07860.08090.08060.02380.151445.91038.79423.8189
20.6669-0.1168-1.00650.14210.1762.0950.28820.10160.0335-0.2628-0.0908-0.1024-0.2334-0.0634-0.15320.6592-0.17910.10230.2713-0.00620.065453.538-0.4188-14.7129
33.62811.2017-0.75671.1348-1.10761.2245-0.4058-0.4982-0.3188-0.22770.0668-0.12510.04830.32820.06950.4286-0.0430.07070.1277-0.03690.166347.7177-17.75296.2098
42.33541.11190.23070.7228-0.19560.4416-0.22840.16050.1579-0.36760.15450.0510.00010.01920.08570.36960.0178-0.06340.1667-0.06710.189121.6937-26.20185.0903
50.7365-0.2840.41830.98340.00910.25570.0597-0.0293-0.068-0.0611-0.15320.0472-0.05150.05590.03530.18390.0070.03250.1565-0.03470.156725.2695-17.359326.4964
60.8161.25010.55015.10931.131.9477-0.24370.0130.3841-1.1282-0.31011.1986-0.2863-0.28320.51710.4640.106-0.19040.1364-0.02380.598923.956421.956826.0229
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND RESID 35:195
2X-RAY DIFFRACTION2CHAIN A AND RESID 196:319
3X-RAY DIFFRACTION3CHAIN B AND RESID 37:158
4X-RAY DIFFRACTION4CHAIN B AND RESID 159:319
5X-RAY DIFFRACTION5CHAIN C AND RESID 35:189
6X-RAY DIFFRACTION6CHAIN C AND RESID 190:319

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