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- PDB-3am2: Clostridium perfringens enterotoxin -

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Basic information

Entry
Database: PDB / ID: 3am2
TitleClostridium perfringens enterotoxin
ComponentsHeat-labile enterotoxin B chain
KeywordsTOXIN / PORE FORMING TOXINS
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 / SAD / Resolution: 2.51 Å
AuthorsKitadokoro, K. / Nishimura, K. / Kamitani, S. / Kimura, J. / Fukui, A. / Abe, H. / Horiguchi, Y.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Crystal Structure of Clostridium perfringens Enterotoxin Displays Features of {beta}-Pore-forming Toxins
Authors: Kitadokoro, K. / Nishimura, K. / Kamitani, S. / Fukui-Miyazaki, A. / Toshima, H. / Abe, H. / Kamata, Y. / Sugita-Konishi, Y. / Yamamoto, S. / Karatani, H. / Horiguchi, Y.
History
DepositionAug 12, 2010Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 13, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,6595
Polymers36,5671
Non-polymers924
Water1,00956
1
A: Heat-labile enterotoxin B chain
hetero molecules

A: Heat-labile enterotoxin B chain
hetero molecules

A: Heat-labile enterotoxin B chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,97615
Polymers109,7003
Non-polymers27612
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area4980 Å2
ΔGint-26 kcal/mol
Surface area38560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.030, 101.030, 101.030
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213
Components on special symmetry positions
IDModelComponents
11A-501-

UNX

21A-502-

UNX

31A-503-

UNX

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Components

#1: Protein Heat-labile enterotoxin B chain


Mass: 36566.547 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium perfringens (bacteria) / Gene: cpe / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / References: UniProt: P01558
#2: Chemical ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 3 / Source method: obtained synthetically
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 56 / 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: 2.55 Å3/Da / Density % sol: 51.78 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 20% PEG 4000, 0.1M Tris-HCl, pH 8, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 98 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: May 25, 2010 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. all: 12081 / Num. obs: 12081 / % possible obs: 99.7 % / Redundancy: 20.7 % / Rmerge(I) obs: 0.087
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 22.5 % / Rmerge(I) obs: 0.478 / Num. unique all: 1199 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.5.0102refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD
Starting model: PDB ENTRY 2QUO

2quo


Resolution: 2.51→45.18 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.925 / SU B: 11.502 / SU ML: 0.255 / Cross valid method: THROUGHOUT / ESU R: 0.549 / ESU R Free: 0.307 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.26924 575 4.8 %RANDOM
Rwork0.21411 ---
obs0.21688 11481 99.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 51.741 Å2
Refinement stepCycle: LAST / Resolution: 2.51→45.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2236 0 9 56 2301
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0222285
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6371.9523104
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.975285
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.16725.429105
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.37415380
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.736157
X-RAY DIFFRACTIONr_chiral_restr0.1070.2352
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021724
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7911.51414
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.58322287
X-RAY DIFFRACTIONr_scbond_it2.2753871
X-RAY DIFFRACTIONr_scangle_it3.4264.5817
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.505→2.57 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.574 39 -
Rwork0.338 857 -
obs-1199 100 %

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