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- PDB-9mui: C. difficile RBD1 with Ca2+ -

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Basic information

Entry
Database: PDB / ID: 9mui
TitleC. difficile RBD1 with Ca2+
ComponentsADP-ribosyltransferase binding component
KeywordsTOXIN / C. difficile / RBD1 / Calcium / CDTb RBD1
Function / homology
Function and homology information


protein homooligomerization / transferase activity / extracellular region / metal ion binding / identical protein binding
Similarity search - Function
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
Similarity search - Domain/homology
ADP-ribosyltransferase binding component
Similarity search - Component
Biological speciesClostridioides difficile (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.29 Å
AuthorsHunter, D. / Pozharski, E.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Commun Biol / Year: 2025
Title: Pore formation by the CDTb component of the Clostridioides difficile binary toxin is Ca 2+ -dependent.
Authors: Abeyawardhane, D.L. / Sevdalis, S.E. / Adipietro, K.A. / Godoy-Ruiz, R. / Varney, K.M. / Nawaz, I.F. / Spittel, A.X. / Hunter, D. / Rustandi, R.R. / Silin, V.I. / des Georges, A. / Cook, M.E. ...Authors: Abeyawardhane, D.L. / Sevdalis, S.E. / Adipietro, K.A. / Godoy-Ruiz, R. / Varney, K.M. / Nawaz, I.F. / Spittel, A.X. / Hunter, D. / Rustandi, R.R. / Silin, V.I. / des Georges, A. / Cook, M.E. / Pozharski, E. / Weber, D.J.
History
DepositionJan 14, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 20, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ADP-ribosyltransferase binding component
B: ADP-ribosyltransferase binding component
C: ADP-ribosyltransferase binding component
D: ADP-ribosyltransferase binding component
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,0288
Polymers57,8684
Non-polymers1604
Water3,063170
1
A: ADP-ribosyltransferase binding component
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,5072
Polymers14,4671
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: ADP-ribosyltransferase binding component
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,5072
Polymers14,4671
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: ADP-ribosyltransferase binding component
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,5072
Polymers14,4671
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: ADP-ribosyltransferase binding component
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,5072
Polymers14,4671
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)119.697, 119.697, 125.091
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
Space group name HallR3
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z
#4: x+1/3,y+2/3,z+2/3
#5: -y+1/3,x-y+2/3,z+2/3
#6: -x+y+1/3,-x+2/3,z+2/3
#7: x+2/3,y+1/3,z+1/3
#8: -y+2/3,x-y+1/3,z+1/3
#9: -x+y+2/3,-x+1/3,z+1/3

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Components

#1: Protein
ADP-ribosyltransferase binding component / CdtB


Mass: 14466.890 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridioides difficile (bacteria) / Gene: cdtB / Production host: Escherichia coli (E. coli) / References: UniProt: A8DS70
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 170 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 2.98 Å3/Da / Density % sol: 58.73 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 30% (w/v) PEG 5000 MME, 100 mM MES/ Sodium hydroxide, 200 mM Ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.95369 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 4, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95369 Å / Relative weight: 1
ReflectionResolution: 2.28→39.91 Å / Num. obs: 29127 / % possible obs: 95.9 % / Redundancy: 7.2 % / Biso Wilson estimate: 43.82 Å2 / CC1/2: 0.983 / Rmerge(I) obs: 0.259 / Rpim(I) all: 0.102 / Rrim(I) all: 0.279 / Net I/σ(I): 4.4
Reflection shellResolution: 2.28→2.36 Å / Redundancy: 5.3 % / Num. unique obs: 2070 / Rpim(I) all: 1.017 / % possible all: 69.2

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Processing

Software
NameVersionClassification
Blu-Ice1.20.1_4487data collection
PHENIX1.20.1_4487refinement
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.29→39.91 Å / SU ML: 0.3587 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 28.7878
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.234 1302 4.5 %
Rwork0.1988 27627 -
obs0.2004 28929 96.18 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 45.19 Å2
Refinement stepCycle: LAST / Resolution: 2.29→39.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4080 0 4 170 4254
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094175
X-RAY DIFFRACTIONf_angle_d0.99325663
X-RAY DIFFRACTIONf_chiral_restr0.0569629
X-RAY DIFFRACTIONf_plane_restr0.0057722
X-RAY DIFFRACTIONf_dihedral_angle_d6.5908550
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.29-2.380.36031430.28862321X-RAY DIFFRACTION74.11
2.38-2.490.32941480.26622929X-RAY DIFFRACTION92.85
2.49-2.620.30061350.22483230X-RAY DIFFRACTION99.97
2.62-2.790.25691610.21063202X-RAY DIFFRACTION100
2.79-30.24351360.20253199X-RAY DIFFRACTION99.97
3-3.30.23051510.18183163X-RAY DIFFRACTION99.4
3.3-3.780.22231370.18423205X-RAY DIFFRACTION99.97
3.78-4.760.20931460.17823198X-RAY DIFFRACTION99.79
4.76-39.910.20461450.20433180X-RAY DIFFRACTION99.46

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