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- PDB-1uyj: Clostridium perfringens epsilon toxin shows structural similarity... -

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Basic information

Entry
Database: PDB / ID: 1uyj
TitleClostridium perfringens epsilon toxin shows structural similarity with the pore forming toxin aerolysin
ComponentsEPSILON-TOXIN
KeywordsTOXIN / BETA PORE FORMING TOXIN
Function / homology
Function and homology information


Dihydrodipicolinate Reductase; domain 2 - #60 / Epsilon toxin / Proaerolysin, chain A, domain 3 / Aerolysin-like toxin / Clostridium epsilon toxin ETX/Bacillus mosquitocidal toxin MTX2 / Proaerolysin; Chain A, domain 3 / Dihydrodipicolinate Reductase; domain 2 / Beta Complex / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
URANIUM ATOM / Epsilaon-toxin
Similarity search - Component
Biological speciesCLOSTRIDIUM PERFRINGENS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.6 Å
AuthorsCole, A.R. / Gibert, M. / Poppoff, M. / Moss, D.S. / Titball, R.W. / Basak, A.K.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2004
Title: Clostridium Perfringens Epsilon-Toxin Shows Structural Similarity to the Pore-Forming Toxin Aerolysin
Authors: Cole, A.R. / Gibert, M. / Popoff, M. / Moss, D.S. / Titball, R.W. / Basak, A.K.
History
DepositionMar 2, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 5, 2004Provider: repository / Type: Initial release
Revision 1.1May 7, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
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_sheet
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_sheet.number_strands
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.
Remark 700 SHEET DETERMINATION METHOD: AUTHOR PROVIDED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: EPSILON-TOXIN
B: EPSILON-TOXIN
C: EPSILON-TOXIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,90415
Polymers99,0473
Non-polymers2,85612
Water93752
1
A: EPSILON-TOXIN
hetero molecules

A: EPSILON-TOXIN
hetero molecules

A: EPSILON-TOXIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,19012
Polymers99,0473
Non-polymers2,1429
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_765-x+y+2,-x+1,z1
crystal symmetry operation2_645-y+1,x-y-1,z1
MethodPQS
2
B: EPSILON-TOXIN
hetero molecules

B: EPSILON-TOXIN
hetero molecules

B: EPSILON-TOXIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,61818
Polymers99,0473
Non-polymers3,57015
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_565-x+y,-x+1,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
MethodPQS
3
C: EPSILON-TOXIN
hetero molecules

C: EPSILON-TOXIN
hetero molecules

C: EPSILON-TOXIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,90415
Polymers99,0473
Non-polymers2,85612
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
crystal symmetry operation2_655-y+1,x-y,z1
MethodPQS
Unit cell
Length a, b, c (Å)125.962, 125.962, 121.862
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63
Components on special symmetry positions
IDModelComponents
11A-2010-

HOH

21B-2012-

HOH

Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1, 0.018, -0.002), (-0.018, 1, -0.019), (0.002, 0.019, 1)-125.0723, 77.71906, -122.35224
2given(0.507, -0.862, 0.01), (-0.862, -0.507, 0.005), (0.001, -0.011, -1)-2.06325, 143.94244, 166.96523
DetailsALTHOUGH IN THE CRYSTAL THE MOLECULE IS A TRIMER THISIS CRYSTALLOGRAPHIC AND NOT RELEVANT BIOLOGICALLY

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Components

#1: Protein EPSILON-TOXIN


Mass: 33015.793 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) CLOSTRIDIUM PERFRINGENS (bacteria) / Variant: TOXINOTYPE D / References: UniProt: Q57398
#2: Chemical
ChemComp-U1 / URANIUM ATOM


Mass: 238.029 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: U
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 52 / 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: 2.6 Å3/Da / Density % sol: 51.6 %
Crystal growpH: 7 / Details: 25% ETHYLENE GLYCOL, pH 7.00

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 1.77, 1.653, 0.885
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 15, 2002 / Details: MIRRORS
RadiationMonochromator: SI(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.771
21.6531
30.8851
ReflectionResolution: 2.6→55.9 Å / Num. obs: 33253 / % possible obs: 98.3 % / Observed criterion σ(I): 2 / Redundancy: 8.91 % / Rmerge(I) obs: 0.045 / Net I/σ(I): 10.0438
Reflection shellResolution: 2.6→2.74 Å / Redundancy: 8.85 % / Rmerge(I) obs: 0.2 / Mean I/σ(I) obs: 2.8 / % possible all: 97.2

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Processing

Software
NameClassification
MOSFLMdata reduction
SCALAdata scaling
SHELXDphasing
SHARPphasing
REFMACrefinement
RefinementMethod to determine structure: MAD / Resolution: 2.6→50 Å / SU B: 12.163 / SU ML: 0.261 / Cross valid method: THROUGHOUT / ESU R Free: 0.342
Details: THE N-TERMINAL 15 RESIDUES ARE DISORDERED, RESIDUES 273 - 279 APPEARED DISORDERED
RfactorNum. reflection% reflectionSelection details
Rfree0.29006 1683 5 %RANDOM
Rwork0.23631 ---
obs0.23905 31967 98.34 %-
Displacement parametersBiso mean: 45.909 Å2
Baniso -1Baniso -2Baniso -3
1-1.16 Å20.58 Å20 Å2
2--1.16 Å20 Å2
3----1.74 Å2
Refinement stepCycle: LAST / Resolution: 2.6→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6256 0 12 52 6320

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