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- PDB-3ziw: Clostridium perfringens enterotoxin, D48A mutation and N-terminal... -

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Basic information

Entry
Database: PDB / ID: 3ziw
TitleClostridium perfringens enterotoxin, D48A mutation and 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 / OTHER / 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 1.3May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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)192,83220
Polymers188,8806
Non-polymers3,95314
Water30,2471679
1
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)96,41610
Polymers94,4403
Non-polymers1,9767
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7640 Å2
ΔGint-41.8 kcal/mol
Surface area45900 Å2
MethodPISA
2
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)96,41610
Polymers94,4403
Non-polymers1,9767
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6740 Å2
ΔGint-34.9 kcal/mol
Surface area45700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)190.660, 128.020, 136.430
Angle α, β, γ (deg.)90.00, 133.81, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.49256, 0.6421, 0.58745), (-0.75604, 0.01861, -0.65426), (-0.43103, -0.7664, 0.47629)-39.33351, -8.97458, -2.94058
2given(0.04453, 0.02759, 0.99863), (0.0348, -0.99905, 0.02605), (0.9984, 0.03359, -0.04544)-47.60131, 49.07594, 47.67242
3given(0.54859, -0.71358, 0.43572), (-0.67144, -0.06546, 0.73816), (-0.49821, -0.69751, -0.51504)-29.58477, 24.87885, 18.61177
4given(-0.44899, -0.74608, 0.49171), (0.73607, 0.00315, 0.6769), (0.50657, 0.66585, 0.54775)-51.27238, 56.61276, 8.47377
5given(-0.49705, -0.73909, -0.45463), (0.63739, 0.04453, -0.76925), (0.58879, -0.67213, 0.44896)-28.81607, 21.71605, 18.78045

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Components

#1: Protein
HEAT-LABILE ENTEROTOXIN B CHAIN


Mass: 31479.953 Da / Num. of mol.: 6 / Fragment: RESIDUES 38-319 / Mutation: YES
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.: 1679 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsD48A MUTATION AND N-TERMINAL 37 RESIDUES DELETED, AND 34GAMG37 INSTEAD OF NATIVE NSNL DUE TO HIS- ...D48A MUTATION AND N-TERMINAL 37 RESIDUES DELETED, AND 34GAMG37 INSTEAD OF NATIVE NSNL DUE TO HIS-TAG REMOVAL SCAR.

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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: ID29 / Wavelength: 1.0332
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 29, 2011 / Details: MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 186226 / % possible obs: 99.1 % / Observed criterion σ(I): 0 / Redundancy: 7.3 % / Biso Wilson estimate: 39.28 Å2 / Rmerge(I) obs: 0.15 / Net I/σ(I): 7.42
Reflection shellResolution: 1.9→1.94 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.86 / Mean I/σ(I) obs: 1.26 / % possible all: 93.1

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Processing

Software
NameVersionClassification
BUSTER2.10.0refinement
XDSdata reduction
XSCALEdata scaling
BUSTERphasing
RefinementMethod to determine structure: OTHER
Starting model: NONE

Resolution: 1.9→49.23 Å / Cor.coef. Fo:Fc: 0.9602 / Cor.coef. Fo:Fc free: 0.9549 / SU R Cruickshank DPI: 0.116 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.12 / SU Rfree Blow DPI: 0.108 / SU Rfree Cruickshank DPI: 0.107
RfactorNum. reflection% reflectionSelection details
Rfree0.1956 9298 5.01 %RANDOM
Rwork0.1749 ---
obs0.176 185455 99.96 %-
Displacement parametersBiso mean: 49.11 Å2
Baniso -1Baniso -2Baniso -3
1-1.6522 Å20 Å2-3.5142 Å2
2--2.535 Å20 Å2
3----4.1872 Å2
Refine analyzeLuzzati coordinate error obs: 0.264 Å
Refinement stepCycle: LAST / Resolution: 1.9→49.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13253 0 185 1679 15117
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0113860HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0918819HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d4814SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes377HARMONIC2
X-RAY DIFFRACTIONt_gen_planes2005HARMONIC5
X-RAY DIFFRACTIONt_it13860HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.77
X-RAY DIFFRACTIONt_other_torsion15.56
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_contact16694SEMIHARMONIC4
LS refinement shellResolution: 1.9→1.95 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2006 643 4.69 %
Rwork0.1929 13062 -
all0.1932 13705 -
obs--99.96 %
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)
10.75830.46010.12772.1601-0.04671.2082-0.1822-0.1170.02440.1445-0.00120.1181-0.175-0.0860.1834-0.02840.02110.0054-0.088-0.0052-0.0005-30.545539.1998-11.1735
21.47050.8275-0.33531.96980.11921.2171-0.03-0.09190.0014-0.029-0.09820.09290.371-0.24950.12810.0058-0.13760.1653-0.0597-0.05290.0296-53.49226.3979-11.4415
30.8859-0.5172-0.48631.08340.17561.2949-0.0769-0.0164-0.0403-0.11780.0311-0.14080.05910.16430.0458-0.058-0.03650.0725-0.0435-0.0179-0.009-5.335122.2498-24.81
42.1008-0.70130.06192.30130.59143.3058-0.3927-0.63540.08360.48050.3263-0.0598-0.1744-0.0090.0665-0.00360.1769-0.0240.0395-0.0409-0.1788-15.519339.1629.4292
51.71860.36010.35992.6194-0.51650.62550.0970.0833-0.40440.0850.0359-0.50030.06190.1069-0.1329-0.07280.0292-0.0289-0.1087-0.080.0642-58.99048.586418.867
61.85360.4091-0.18462.622-0.73581.9808-0.07990.37460.3303-0.44230.031-0.3251-0.14950.05590.0489-0.0172-0.03340.1103-0.04430.0581-0.0508-61.20540.3471-5.013
70.90730.49790.41241.0810.1211.9515-0.08870.23820.0492-0.1540.12910.0539-0.0659-0.0325-0.0404-0.04410.0154-0.0278-0.0025-0.0022-0.1012-79.215634.643912.3122
81.71950.38060.42562.34440.10661.9732-0.0057-0.27980.19320.3463-0.0364-0.0652-0.41590.08950.0420.08180.0043-0.0395-0.0815-0.0569-0.1534-68.625151.907246.4919
91.7440.1393-0.16021.05090.53661.26670.096-0.2315-0.02340.1348-0.03610.0438-0.0464-0.0272-0.0598-0.00950.00920.0017-0.03110.0252-0.1202-72.132926.59244.1064
104.436-0.3159-0.43561.9730.35631.15310.121-0.1167-0.6020.04310.1815-0.49970.040.5065-0.3025-0.20750.0605-0.08910.0265-0.14980.1041-37.98829.570333.6647
111.90230.0159-0.04281.3602-0.04581.11830.07040.09420.1218-0.1686-0.00230.263-0.0065-0.3063-0.0681-0.0517-0.0346-0.008-0.06170.0084-0.048-37.405712.5088-30.6288
123.15060.49230.00352.9138-0.70941.56830.072-0.3995-0.5971-0.1596-0.2296-0.61410.29540.31390.1576-0.10130.02970.0465-0.07280.10870.0827-1.9164-3.3117-22.3359
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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