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- PDB-2j3v: Crystal structure of the enzymatic component C2-I of the C2-toxin... -

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Basic information

Entry
Database: PDB / ID: 2j3v
TitleCrystal structure of the enzymatic component C2-I of the C2-toxin from Clostridium botulinum at pH 3.0
ComponentsC2 TOXIN COMPONENT I
KeywordsTOXIN / ADP-RIBOSYLTRANSFERASE / CLOSTRIDIUM BOTULINUM
Function / homology
Function and homology information


extracellular region
Similarity search - Function
Binary exotoxin A, clostridial type / Toxin ADP-ribosyltransferase; Chain A, domain 1 / Toxin ADP-ribosyltransferase; Chain A, domain 1 / ADP ribosyltransferase / ADP-ribosyltransferase exoenzyme / Toxin-related mono-ADP-ribosyltransferase (TR mART) core domain profile. / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
C2 toxin (Component I)
Similarity search - Component
Biological speciesCLOSTRIDIUM BOTULINUM (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.11 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 23, 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 1.3May 8, 2019Group: Data collection / Experimental preparation / Other
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.4May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.
Remark 700 SHEET DETERMINATION METHOD: AUTHOR PROVIDED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: C2 TOXIN COMPONENT I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,08930
Polymers49,3631
Non-polymers2,72629
Water5,855325
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)114.811, 114.811, 162.681
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322

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Components

#1: Protein C2 TOXIN COMPONENT I / ADP-RIBOSYLTRANSFERASE C2-I


Mass: 49362.555 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CLOSTRIDIUM BOTULINUM (bacteria) / Plasmid: PET-3B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: O69275
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 325 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, LYS 20 TO GLU

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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: 3.15 Å3/Da / Density % sol: 61 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 3
Details: PROTEIN: 10 MG/ML IN H2O RESERVOIR: 0.8 M (NH4)2SO4, 0.1 M CITRATE PH 3.0, HANGING DROP:1:1

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9801
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9801 Å / Relative weight: 1
ReflectionResolution: 2.12→85 Å / Num. obs: 36331 / % possible obs: 99.1 % / Observed criterion σ(I): -3 / Redundancy: 10.4 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 30.9
Reflection shellResolution: 2.12→2.21 Å / Rmerge(I) obs: 0.2 / Mean I/σ(I) obs: 8.9 / % possible all: 97.5

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
SHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 2.11→19.32 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.921 / Cross valid method: THROUGHOUT / ESU R: 0.191 / ESU R Free: 0.176 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.238 2544 7 %RANDOM
Rwork0.188 ---
obs0.191 33796 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 25.62 Å2
Baniso -1Baniso -2Baniso -3
1-2.29 Å21.15 Å20 Å2
2--2.29 Å20 Å2
3----3.44 Å2
Refinement stepCycle: LAST / Resolution: 2.11→19.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3474 0 160 325 3959
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0223666
X-RAY DIFFRACTIONr_bond_other_d00.023285
X-RAY DIFFRACTIONr_angle_refined_deg1.9011.9994929
X-RAY DIFFRACTIONr_angle_other_deg3.70737703
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.65429
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.64825.543175
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.73615668
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.9331517
X-RAY DIFFRACTIONr_chiral_restr0.1110.2536
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023888
X-RAY DIFFRACTIONr_gen_planes_other0.0090.02685
X-RAY DIFFRACTIONr_nbd_refined0.2210.2769
X-RAY DIFFRACTIONr_nbd_other0.2430.23033
X-RAY DIFFRACTIONr_nbtor_refined0.1840.21777
X-RAY DIFFRACTIONr_nbtor_other0.1130.21814
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1810.2291
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1740.232
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2640.284
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2440.235
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8961.52142
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.66323488
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.68931524
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.2964.51441
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.11→2.16 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.449 164
Rwork0.427 2188

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