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- PDB-2yhj: Clostridium perfringens Enterotoxin at 4.0 Angstrom Resolution -

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Basic information

Entry
Database: PDB / ID: 2yhj
TitleClostridium perfringens Enterotoxin at 4.0 Angstrom Resolution
ComponentsHEAT-LABILE ENTEROTOXIN B CHAIN
KeywordsTOXIN / PORE-FORMING TOXIN / 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
Heat-labile enterotoxin B chain
Similarity search - Component
Biological speciesCLOSTRIDIUM PERFRINGENS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4 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: Crystallization and Preliminary Crystallographic Analysis of the Clostridium Perfringens Enterotoxin.
Authors: Briggs, D.C. / Smedley III, J.G. / Mcclane, B.A. / Basak, A.K.
History
DepositionMay 3, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 17, 2011Provider: repository / Type: Initial release
Revision 1.1Oct 12, 2011Group: Database references
Revision 1.2Aug 13, 2014Group: Other
Revision 1.3Dec 20, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HEAT-LABILE ENTEROTOXIN B CHAIN
B: HEAT-LABILE ENTEROTOXIN B CHAIN


Theoretical massNumber of molelcules
Total (without water)70,6902
Polymers70,6902
Non-polymers00
Water00
1
A: HEAT-LABILE ENTEROTOXIN B CHAIN

A: HEAT-LABILE ENTEROTOXIN B CHAIN

A: HEAT-LABILE ENTEROTOXIN B CHAIN


Theoretical massNumber of molelcules
Total (without water)106,0363
Polymers106,0363
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation9_555y,z,x1
crystal symmetry operation5_555z,x,y1
Buried area5140 Å2
ΔGint-17.7 kcal/mol
Surface area37120 Å2
MethodPISA
2
B: HEAT-LABILE ENTEROTOXIN B CHAIN

B: HEAT-LABILE ENTEROTOXIN B CHAIN

B: HEAT-LABILE ENTEROTOXIN B CHAIN


Theoretical massNumber of molelcules
Total (without water)106,0363
Polymers106,0363
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation9_555y,z,x1
crystal symmetry operation5_555z,x,y1
Buried area5130 Å2
ΔGint-16.6 kcal/mol
Surface area37390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)159.697, 159.697, 159.697
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.00405, -0.99991, 0.01284), (-0.99995, 0.00394, -0.00912), (0.00907, -0.01288, -0.99988)
Vector: -39.63819, -40.20411, -40.29426)

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Components

#1: Protein HEAT-LABILE ENTEROTOXIN B CHAIN


Mass: 35345.207 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) CLOSTRIDIUM PERFRINGENS (bacteria) / Strain: NCTC 8239 / References: UniProt: P01558

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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: 4.8 Å3/Da / Density % sol: 75 % / Description: NONE
Crystal growpH: 4.3
Details: 10 MG/ML PROTEIN IN WATER EQUILIBRATED AGAINST 2.0 M HEXANE-1,2-DIOL AND 10 MM ZNCL2 IN 50 MM CITRATE, PH 4.3 .

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 1.2823
DetectorType: ADSC CCD / Detector: CCD / Date: Jul 2, 2003 / Details: MIRRORS
RadiationMonochromator: SI CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2823 Å / Relative weight: 1
ReflectionResolution: 4→70 Å / Num. obs: 11712 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 10 % / Biso Wilson estimate: 85.23 Å2 / Rmerge(I) obs: 0.17 / Net I/σ(I): 16.7
Reflection shellResolution: 4→4.2 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.62 / Mean I/σ(I) obs: 3.2 / % possible all: 99.5

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Processing

Software
NameVersionClassification
BUSTER2.8.0refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2XH6, CHAIN A

2xh6


Resolution: 4→65.2 Å / Cor.coef. Fo:Fc: 0.8563 / Cor.coef. Fo:Fc free: 0.7484 / Cross valid method: THROUGHOUT / σ(F): 0 / Details: THERE IS NO ELECTRON DENSITY FOR RESIDUES 1-34
RfactorNum. reflection% reflectionSelection details
Rfree0.2995 555 4.74 %RANDOM
Rwork0.2468 ---
obs0.2492 11707 --
Displacement parametersBiso mean: 115.4 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyzeLuzzati coordinate error obs: 1.025 Å
Refinement stepCycle: LAST / Resolution: 4→65.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4416 0 0 0 4416
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0074504HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.036132HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1512SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes126HARMONIC2
X-RAY DIFFRACTIONt_gen_planes648HARMONIC5
X-RAY DIFFRACTIONt_it4504HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.52
X-RAY DIFFRACTIONt_other_torsion17.7
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion612SEMIHARMONIC5
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_contact4877SEMIHARMONIC4
LS refinement shellResolution: 4→4.38 Å / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.3078 129 4.72 %
Rwork0.2539 2603 -
all0.2564 2732 -

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