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- PDB-2f6e: Clostridium difficile Toxin A C-terminal fragment 1 (TcdA-f1) -

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Basic information

Entry
Database: PDB / ID: 2f6e
TitleClostridium difficile Toxin A C-terminal fragment 1 (TcdA-f1)
ComponentsToxin A
KeywordsTOXIN / beta solenoid / C-terminal repetitive domain / CROPs
Function / homology
Function and homology information


host cell cytosol / Transferases; Glycosyltransferases; Hexosyltransferases / glycosyltransferase activity / cysteine-type peptidase activity / host cell endosome membrane / toxin activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / lipid binding / host cell plasma membrane / proteolysis ...host cell cytosol / Transferases; Glycosyltransferases; Hexosyltransferases / glycosyltransferase activity / cysteine-type peptidase activity / host cell endosome membrane / toxin activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / lipid binding / host cell plasma membrane / proteolysis / extracellular region / metal ion binding / membrane
Similarity search - Function
Cholin Binding / left handed beta-beta-3-solenoid / TcdA/TcdB toxin, pore forming domain / TcdA/TcdB pore forming domain / CGT/MARTX, cysteine protease (CPD) domain / CGT/MARTX, cysteine protease (CPD) domain superfamily / Peptidase C80 family / CGT/MARTX cysteine protease (CPD) domain profile. / TcdA/TcdB toxin, N-terminal helical domain / TcdB toxin N-terminal helical domain ...Cholin Binding / left handed beta-beta-3-solenoid / TcdA/TcdB toxin, pore forming domain / TcdA/TcdB pore forming domain / CGT/MARTX, cysteine protease (CPD) domain / CGT/MARTX, cysteine protease (CPD) domain superfamily / Peptidase C80 family / CGT/MARTX cysteine protease (CPD) domain profile. / TcdA/TcdB toxin, N-terminal helical domain / TcdB toxin N-terminal helical domain / TcdA/TcdB toxin, catalytic glycosyltransferase domain / TcdA/TcdB catalytic glycosyltransferase domain / Choline-binding repeat / Putative cell wall binding repeat / Cell wall/choline-binding repeat / Cell wall-binding repeat profile. / Nucleotide-diphospho-sugar transferases / Ribbon / Mainly Beta
Similarity search - Domain/homology
Biological speciesClostridium difficile (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.85 Å
AuthorsNg, K.K. / Ho, J.G.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2005
Title: Crystal structure of receptor-binding C-terminal repeats from Clostridium difficile toxin A
Authors: Ho, J.G. / Greco, A. / Rupnik, M. / Ng, K.K.
History
DepositionNov 29, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 20, 2005Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Dec 21, 2022Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Remark 999Sequence The differences between the sequence present in this structure and the sequence in the ...Sequence The differences between the sequence present in this structure and the sequence in the reference database are unique to strain 48489 of Clostridium difficile.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Toxin A


Theoretical massNumber of molelcules
Total (without water)14,1981
Polymers14,1981
Non-polymers00
Water3,009167
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.050, 42.050, 132.110
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Toxin A


Mass: 14197.847 Da / Num. of mol.: 1 / Fragment: C-terminal fragment 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium difficile (bacteria) / Strain: 48489 / Gene: toxA, tcdA / Plasmid: pET-3a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P16154
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 167 / 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: 2.06 Å3/Da / Density % sol: 40.17 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 250 mM ammonium tartrate, 100 mM sodium acetate, 20% glycerol, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 0.979571,0.979741,1.019867
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 15, 2004
RadiationMonochromator: double crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9795711
20.9797411
31.0198671
ReflectionResolution: 1.85→40.16 Å / Num. all: 10716 / Num. obs: 10716 / % possible obs: 99.3 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 6.4 % / Biso Wilson estimate: 15 Å2 / Rmerge(I) obs: 0.057 / Rsym value: 0.057 / Net I/σ(I): 21.4
Reflection shellResolution: 1.85→1.92 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.187 / Mean I/σ(I) obs: 7.4 / Num. unique all: 1015 / Rsym value: 0.187 / % possible all: 95.7

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.85→40.16 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.933 / SU B: 2.436 / SU ML: 0.077 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.137 / ESU R Free: 0.13 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.205 516 4.8 %RANDOM
Rwork0.15979 ---
all0.16191 10199 --
obs0.16191 10199 99.04 %-
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: 13.84 Å2
Baniso -1Baniso -2Baniso -3
1-0.1 Å20 Å20 Å2
2--0.1 Å20 Å2
3----0.2 Å2
Refinement stepCycle: LAST / Resolution: 1.85→40.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms988 0 0 167 1155
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0221019
X-RAY DIFFRACTIONr_angle_refined_deg0.9961.9151382
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3285124
X-RAY DIFFRACTIONr_chiral_restr0.0740.2133
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.02835
X-RAY DIFFRACTIONr_nbd_refined0.1850.2393
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1270.2110
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1740.251
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1210.223
X-RAY DIFFRACTIONr_mcbond_it1.962613
X-RAY DIFFRACTIONr_mcangle_it2.9292.5972
X-RAY DIFFRACTIONr_scbond_it3.933.5406
X-RAY DIFFRACTIONr_scangle_it5.7454.5410
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection
Rfree0.175 43
Rwork0.135 709
obs-752
Refinement TLS params.Method: refined / Origin x: 18.3848 Å / Origin y: 16.1024 Å / Origin z: 44.383 Å
111213212223313233
T0.008 Å2-0.0011 Å2-0.0004 Å2-0.0056 Å20.0019 Å2--0.007 Å2
L0.1326 °20.0672 °20.0296 °2-0.2584 °20.2549 °2--0.3118 °2
S-0.0143 Å °0.0144 Å °0.0059 Å °0.0123 Å °0.031 Å °0.013 Å °-0.0005 Å °0.0049 Å °-0.0166 Å °

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