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- PDB-3zix: Clostridium perfringens Enterotoxin with the N-terminal 37 residu... -

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Basic information

Entry
Database: PDB / ID: 3zix
TitleClostridium perfringens Enterotoxin with the N-terminal 37 residues deleted
ComponentsHEAT-LABILE ENTEROTOXIN B CHAIN
KeywordsTOXIN / BETA PORE-FORMING-TOXIN / CYTOTOXICITY MUTANT
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
Heat-labile enterotoxin B chain
Similarity search - Component
Biological speciesCLOSTRIDIUM PERFRINGENS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsYelland, T. / Naylor, C.E. / Savva, C.G. / Basak, A.K.
Citation
Journal: J.Mol.Biol. / Year: 2014
Title: Structure of a C. Perfringens Enterotoxin Mutant in Complex with a Modified Claudin-2 Extracellular Loop 2
Authors: Yelland, T.S. / Naylor, C.E. / Bagoban, T. / Savva, C.G. / Moss, D.S. / Mcclane, B.A. / Blasig, I.E. / Popoff, M. / Basak, A.K.
#1: 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. / Moss, D.S. / Mcclane, B.A. / Basak, A.K.
History
DepositionJan 14, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 29, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 23, 2014Group: Database references
Revision 1.2Aug 27, 2014Group: Database references
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / 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 / _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: HEAT-LABILE ENTEROTOXIN B CHAIN
B: HEAT-LABILE ENTEROTOXIN B CHAIN
C: HEAT-LABILE ENTEROTOXIN B CHAIN
D: HEAT-LABILE ENTEROTOXIN B CHAIN
E: HEAT-LABILE ENTEROTOXIN B CHAIN
F: HEAT-LABILE ENTEROTOXIN B CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)193,09620
Polymers189,1446
Non-polymers3,95314
Water31,7241761
1
A: HEAT-LABILE ENTEROTOXIN B CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,3714
Polymers31,5241
Non-polymers8473
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)32,0893
Polymers31,5241
Non-polymers5652
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: HEAT-LABILE ENTEROTOXIN B CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,0893
Polymers31,5241
Non-polymers5652
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: HEAT-LABILE ENTEROTOXIN B CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,0893
Polymers31,5241
Non-polymers5652
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: HEAT-LABILE ENTEROTOXIN B CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,3714
Polymers31,5241
Non-polymers8473
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: HEAT-LABILE ENTEROTOXIN B CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,0893
Polymers31,5241
Non-polymers5652
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)191.680, 128.290, 137.200
Angle α, β, γ (deg.)90.00, 133.81, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
HEAT-LABILE ENTEROTOXIN B CHAIN


Mass: 31523.965 Da / Num. of mol.: 6 / Fragment: RESIDUES 38-319
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CLOSTRIDIUM PERFRINGENS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P01558
#2: Chemical
ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 282.331 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1761 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsN-TERMINAL 37 RESIDUES DELETED, 34GAMG37 PRESENT AT N- TERMINAL IS THE RESULT OF PROTEASE CLEAVAGE ...N-TERMINAL 37 RESIDUES DELETED, 34GAMG37 PRESENT AT N- TERMINAL IS THE RESULT OF PROTEASE CLEAVAGE SCAR FROM PURIFICATION.

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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: 2.9 Å3/Da / Density % sol: 58 % / Description: NONE
Crystal growpH: 6 / Details: 25 % PEG 1500, 0.1 M SPG BUFFER, PH 6.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 11, 2011 / Details: PT-COATED MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 1.9→47.03 Å / Num. obs: 189121 / % possible obs: 98.2 % / Observed criterion σ(I): 0 / Redundancy: 7.7 % / Biso Wilson estimate: 35.62 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 17.4
Reflection shellResolution: 1.9→1.94 Å / Redundancy: 7.3 % / Rmerge(I) obs: 1.22 / Mean I/σ(I) obs: 1.6 / % possible all: 95.1

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Processing

Software
NameVersionClassification
BUSTER2.10.0refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2XH6

2xh6


Resolution: 1.9→47.03 Å / Cor.coef. Fo:Fc: 0.9605 / Cor.coef. Fo:Fc free: 0.9549 / SU R Cruickshank DPI: 0.118 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.122 / SU Rfree Blow DPI: 0.11 / SU Rfree Cruickshank DPI: 0.108
RfactorNum. reflection% reflectionSelection details
Rfree0.197 9299 5.01 %RANDOM
Rwork0.1764 ---
obs0.1775 185641 98.8 %-
Displacement parametersBiso mean: 45.55 Å2
Baniso -1Baniso -2Baniso -3
1-1.5734 Å20 Å2-3.708 Å2
2--0.9007 Å20 Å2
3----2.4742 Å2
Refine analyzeLuzzati coordinate error obs: 0.277 Å
Refinement stepCycle: LAST / Resolution: 1.9→47.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13271 0 185 1761 15217
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0113878HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0818843HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d4826SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes383HARMONIC2
X-RAY DIFFRACTIONt_gen_planes2005HARMONIC5
X-RAY DIFFRACTIONt_it13878HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.81
X-RAY DIFFRACTIONt_other_torsion15.86
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1866SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact16284SEMIHARMONIC4
LS refinement shellResolution: 1.9→1.95 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2407 656 4.84 %
Rwork0.2131 12894 -
all0.2145 13550 -
obs--98.8 %
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)
10.90980.27260.19151.78890.30971.1554-0.1777-0.15360.0910.1423-0.00770.149-0.1417-0.12360.1854-0.05710.01470.0003-0.0847-0.00880.0068-30.84839.1671-11.307
21.53681.1579-0.35172.40280.32631.32690.0714-0.13780.02250.1644-0.1390.34360.3136-0.31920.0677-0.0508-0.17360.1836-0.039-0.03850.0558-53.87556.3558-11.7969
30.9445-0.6208-0.54811.23420.37291.4272-0.0756-0.033-0.0573-0.11010.0428-0.14220.05560.21160.0328-0.0711-0.03310.0639-0.0343-0.0117-0.0239-5.372522.2732-24.9446
42.369-0.5984-0.0361.78360.5382.1229-0.3431-0.76950.150.37530.2873-0.049-0.09390.0160.0559-0.04910.1619-0.01320.1315-0.0553-0.1801-15.834538.89099.514
51.7220.39380.46512.5118-0.47071.00520.14390.134-0.46970.12620.0421-0.58150.0860.1624-0.186-0.10520.0296-0.0563-0.107-0.10020.1083-59.30678.556818.7406
61.95490.2557-0.01652.6144-0.81061.9374-0.18470.47960.3484-0.37080.1255-0.3444-0.24290.13050.0592-0.04-0.10940.11770.010.0508-0.0893-61.763440.3681-5.1991
70.83960.41010.44610.84430.16491.6706-0.09680.24940.0493-0.12720.11640.0425-0.10160.0035-0.0196-0.03150.0107-0.02070.00430.0001-0.0859-79.741634.666912.4103
81.53350.33090.26032.38390.13631.8250.0322-0.27750.21970.3665-0.0552-0.0721-0.31420.10230.0230.0754-0.0162-0.032-0.076-0.0607-0.1258-69.068451.916346.7872
92.13970.1257-0.17751.00850.52791.09480.106-0.289-0.02020.1924-0.050.0548-0.04520.0069-0.056-0.00770.00420.008-0.04840.0293-0.1152-72.487326.497144.3567
104.0653-0.3948-0.37831.85930.49191.82870.11530.0565-0.60830.050.1802-0.47260.04650.6157-0.2955-0.22640.0657-0.11020.0476-0.14760.0869-38.21259.601533.6399
111.6732-0.0001-0.0461.479-0.08461.13760.04630.09950.0677-0.14850.02140.32080.0179-0.3223-0.0678-0.0936-0.0305-0.0191-0.07490.0192-0.0344-37.501912.4383-30.9469
123.30730.5137-0.31643.0268-0.71221.4494-0.0295-0.4401-0.6364-0.166-0.194-0.61320.21280.3320.2235-0.13610.05180.0555-0.07030.13480.0916-1.8533-3.1848-22.2249
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{A|34 - 193}
2X-RAY DIFFRACTION2{A|194 - 319}
3X-RAY DIFFRACTION3{B|34 - 193}
4X-RAY DIFFRACTION4{B|194 - 319}
5X-RAY DIFFRACTION5{C|34 - 193}
6X-RAY DIFFRACTION6{C|194 - 319}
7X-RAY DIFFRACTION7{D|34 - 193}
8X-RAY DIFFRACTION8{D|194 - 319}
9X-RAY DIFFRACTION9{E|34 - 193}
10X-RAY DIFFRACTION10{E|194 - 319}
11X-RAY DIFFRACTION11{F|34 - 193}
12X-RAY DIFFRACTION12{F|194 - 319}

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