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- PDB-9bja: C. difficile Tcdb cysteine protease domain in complex with IP6 -

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Basic information

Entry
Database: PDB / ID: 9bja
TitleC. difficile Tcdb cysteine protease domain in complex with IP6
ComponentsToxin B
KeywordsTOXIN / catalytic activity peptidase activity catalytic activity / acting on a protein toxin activity small molecule binding
Function / homology
Function and homology information


glucosyltransferase activity / host cell cytosol / Transferases; Glycosyltransferases; Hexosyltransferases / 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 ...glucosyltransferase activity / host cell cytosol / Transferases; Glycosyltransferases; Hexosyltransferases / 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 / membrane / metal ion binding
Similarity search - Function
TcdA/TcdB toxin, N-terminal helical domain / TcdB toxin N-terminal helical domain / TcdA/TcdB toxin, catalytic glycosyltransferase domain / TcdA/TcdB catalytic glycosyltransferase domain / Dermonecrotic/RTX toxin, membrane localization domain / Membrane Localization Domain / TcdA/TcdB toxin, pore forming domain / TcdA/TcdB pore forming domain / CGT/MARTX, cysteine protease (CPD) domain / CGT/MARTX, cysteine protease (CPD) domain superfamily ...TcdA/TcdB toxin, N-terminal helical domain / TcdB toxin N-terminal helical domain / TcdA/TcdB toxin, catalytic glycosyltransferase domain / TcdA/TcdB catalytic glycosyltransferase domain / Dermonecrotic/RTX toxin, membrane localization domain / Membrane Localization Domain / 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. / Choline-binding repeat / Putative cell wall binding repeat / Cell wall/choline-binding repeat / Cell wall-binding repeat profile. / Nucleotide-diphospho-sugar transferases
Similarity search - Domain/homology
INOSITOL HEXAKISPHOSPHATE / Toxin B
Similarity search - Component
Biological speciesClostridioides difficile (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsVeyron, S. / Cummer, R.
Funding support Canada, 2items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)PJT-173262 Canada
Natural Sciences and Engineering Research Council (NSERC, Canada)RGPIN-2020-04908 Canada
CitationJournal: Chemrxiv / Year: 2024
Title: Structure-activity relationship of inositol thiophosphate analogs as allosteric activators of Clostridioides difficile Toxin B
Authors: Cummer, R. / Grosjean, F. / Bolteau, R. / Vasegh, S.E. / Veyron, S. / Keogh, L. / Trempe, J.-F. / Castagner, B.
History
DepositionApr 25, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 3, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Toxin B
B: Toxin B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,0494
Polymers59,7292
Non-polymers1,3202
Water3,585199
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.051, 89.171, 67.597
Angle α, β, γ (deg.)90.000, 103.780, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and ((resid 5 through 6 and (name N...
d_2ens_1(chain "B" and (resid 5 through 16 or (resid 17...

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11ASNASNGLNGLNAA5 - 666 - 67
d_12ASNASNPHEPHEAA68 - 11569 - 116
d_13THRTHRTYRTYRAA117 - 160118 - 161
d_14ILEILEARGARGAA162 - 202163 - 203
d_15ASNASNASPASPAA204 - 213205 - 214
d_16SERSERSERSERAA215 - 230216 - 231
d_17LYSLYSPROPROAA232 - 252233 - 253
d_18IHPIHPIHPIHPAC301
d_21ASNASNGLNGLNBB5 - 666 - 67
d_22ASNASNPHEPHEBB68 - 11569 - 116
d_23THRTHRTYRTYRBB117 - 160118 - 161
d_24ILEILEARGARGBB162 - 202163 - 203
d_25ASNASNASPASPBB204 - 213205 - 214
d_26SERSERSERSERBB215 - 230216 - 231
d_27LYSLYSPROPROBB232 - 252233 - 253
d_28IHPIHPIHPIHPBD301

NCS oper: (Code: givenMatrix: (-0.999713018047, 0.023100743894, -0.00634327823668), (0.023280667646, 0.999280837131, -0.0299302365067), (0.00564730565827, -0.0300693228214, -0.999531862305)Vector: 29. ...NCS oper: (Code: given
Matrix: (-0.999713018047, 0.023100743894, -0.00634327823668), (0.023280667646, 0.999280837131, -0.0299302365067), (0.00564730565827, -0.0300693228214, -0.999531862305)
Vector: 29.8692644756, 1.65152705244, -31.7504398893)

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Components

#1: Protein Toxin B


Mass: 29864.479 Da / Num. of mol.: 2 / Fragment: Cysteine protease domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridioides difficile (bacteria) / Strain: 342 / Gene: tcdB, toxB / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P18177, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases
#2: Chemical ChemComp-IHP / INOSITOL HEXAKISPHOSPHATE / MYO-INOSITOL HEXAKISPHOSPHATE / INOSITOL 1,2,3,4,5,6-HEXAKISPHOSPHATE


Mass: 660.035 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H18O24P6 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 199 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.26 Å3/Da / Density % sol: 45.52 %
Crystal growTemperature: 295 K / Method: vapor diffusion
Details: 0.1 M Tris HCl, pH 8.2, 36% (w/v) PEG2000 monomethyl ether

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.95371 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jun 7, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95371 Å / Relative weight: 1
ReflectionResolution: 2.1→89.17 Å / Num. obs: 29657 / % possible obs: 99.9 % / Redundancy: 6.7 % / Biso Wilson estimate: 34.04 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.106 / Rpim(I) all: 0.048 / Net I/σ(I): 9.3
Reflection shellResolution: 2.1→2.16 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.545 / Mean I/σ(I) obs: 3.1 / Num. unique obs: 2423 / CC1/2: 0.911 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
BUSTER2.10.4refinement
autoPROCdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→52.87 Å / SU ML: 0.2728 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 30.4459
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2574 1496 5.06 %Random
Rwork0.2281 28055 --
obs0.2296 29551 99.62 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 44.25 Å2
Refinement stepCycle: LAST / Resolution: 2.1→52.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3917 0 72 199 4188
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00994098
X-RAY DIFFRACTIONf_angle_d1.2095567
X-RAY DIFFRACTIONf_chiral_restr0.0747626
X-RAY DIFFRACTIONf_plane_restr0.015700
X-RAY DIFFRACTIONf_dihedral_angle_d15.85091537
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.5523832412 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.170.30561410.28982543X-RAY DIFFRACTION100
2.17-2.250.34951200.27822539X-RAY DIFFRACTION99.85
2.25-2.340.32381660.27112531X-RAY DIFFRACTION99.7
2.34-2.440.27211340.26672538X-RAY DIFFRACTION99.7
2.44-2.570.31741290.26592542X-RAY DIFFRACTION99.85
2.57-2.730.2711390.2752554X-RAY DIFFRACTION99.7
2.73-2.940.24711330.2712556X-RAY DIFFRACTION99.19
2.94-3.240.26851180.24892553X-RAY DIFFRACTION99.63
3.24-3.710.25691420.21792546X-RAY DIFFRACTION99.33
3.71-4.670.21481440.18062548X-RAY DIFFRACTION99.74
4.67-52.870.23371300.19482605X-RAY DIFFRACTION99.13

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