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- PDB-2j42: low quality crystal structure of the transport component C2-II of... -

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Basic information

Entry
Database: PDB / ID: 2j42
Titlelow quality crystal structure of the transport component C2-II of the C2-toxin from Clostridium botulinum
ComponentsC2 TOXIN COMPONENT-II
KeywordsTOXIN / CLOSTRIDIUM BOTULINUM / C2-II
Function / homology
Function and homology information


protein homooligomerization / extracellular region
Similarity search - Function
Toxin - Anthrax Protective Antigen; domain 1 / Toxin - Anthrax Protective Antigen;domain 1 / Ubiquitin-like (UB roll) - #110 / Protective antigen, heptamerisation domain / Bacterial exotoxin B / Protective antigen, heptamerisation domain / Protective antigen, Ca-binding domain / Clostridial binary toxin B/anthrax toxin PA, domain 3 / Protective antigen, heptamerisation domain superfamily / Clostridial binary toxin B/anthrax toxin PA Ca-binding domain ...Toxin - Anthrax Protective Antigen; domain 1 / Toxin - Anthrax Protective Antigen;domain 1 / Ubiquitin-like (UB roll) - #110 / Protective antigen, heptamerisation domain / Bacterial exotoxin B / Protective antigen, heptamerisation domain / Protective antigen, Ca-binding domain / Clostridial binary toxin B/anthrax toxin PA, domain 3 / Protective antigen, heptamerisation domain superfamily / Clostridial binary toxin B/anthrax toxin PA Ca-binding domain / Clostridial binary toxin B/anthrax toxin PA domain 2 / Clostridial binary toxin B/anthrax toxin PA domain 3 / PA14 domain / PA14 / PA14 domain / Ubiquitin-like (UB roll) / Jelly Rolls / Roll / Alpha-Beta Complex / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
C2 toxin (Component-II)
Similarity search - Component
Biological speciesCLOSTRIDIUM BOTULINUM (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.13 Å
AuthorsSchleberger, C. / Hochmann, H. / Barth, H. / Aktories, K. / Schulz, G.E.
CitationJournal: J.Mol.Biol. / Year: 2006
Title: Structure and Action of the Binary C2 Toxin from Clostridium Botulinum.
Authors: Schleberger, C. / Hochmann, H. / Barth, H. / Aktories, K. / Schulz, G.E.
History
DepositionAug 24, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 11, 2006Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 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
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: C2 TOXIN COMPONENT-II


Theoretical massNumber of molelcules
Total (without water)80,7671
Polymers80,7671
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)104.400, 104.400, 153.200
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein C2 TOXIN COMPONENT-II / C2-II


Mass: 80766.562 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CLOSTRIDIUM BOTULINUM (bacteria) / Plasmid: PGEX-2T / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: O86171

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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: 52 %
Crystal growpH: 4.6
Details: PROTEIN: 3 MG/ML IN H2O RESERVOIR: 0.1 M SODIUM ACETATE PH 4.6, 1.5 M (NH4)2SO4, 5 % ISOPROPANOL, 3 % ETHANOL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9795
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 3.1→40 Å / Num. obs: 15486 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 9.5 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 21.5
Reflection shellResolution: 3.13→3.22 Å / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 5.7 / % possible all: 100

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Processing

Software
NameVersionClassification
TNTBUSTER/TNTrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ACC

1acc


Resolution: 3.13→30 Å / Cross valid method: THROUGHOUT / σ(F): 0
Details: INCOMPLETE MODEL, MISSING ATOM STRUCTURE WAS USED. MODEL IS OF LOW QUALITY DUE TO THE LOW RESOLUTION, NO FURTHER REFINEMENT WAS POSSIBLE.
RfactorNum. reflection% reflectionSelection details
Rfree0.4326 774 5 %0.4137
Rwork0.4127 ---
obs0.4127 14703 --
Refinement stepCycle: LAST / Resolution: 3.13→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3948 0 0 0 3948

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