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- PDB-8ssm: Citrobacter rodentium contact dependent growth inhibition (CDI) t... -

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Basic information

Entry
Database: PDB / ID: 8ssm
TitleCitrobacter rodentium contact dependent growth inhibition (CDI) toxin (CdiA-CT) and immunity (CdiI) complex
Components
  • CdiI (immunity protein)
  • Contact-dependent inhibitor A
KeywordsTOXIN / Immunity protein / Peptidase
Function / homology
Function and homology information


catalytic activity / toxin activity
Similarity search - Function
Toxin CdiA-like, Filamentous hemagglutinin motif repeats / VENN motif-containing domain / Pre-toxin domain with VENN motif / Hemagglutinin repeat / Hemagglutinin repeat / Pectin lyase fold / Pectin lyase fold/virulence factor / BRCT domain profile. / BRCT domain
Similarity search - Domain/homology
Fimbrial usher protein StbD / Uncharacterized protein
Similarity search - Component
Biological speciesCitrobacter rodentium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.48 Å
AuthorsCuthbert, B.J. / Goulding, C.W. / Hayes, C.S. / Nhan, D.Q.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: To Be Published
Title: Structural and biochemical studies into Citrobacter rodentium contact dependent growth inhibition (CDI) peptidase toxin
Authors: Cuthbert, B.J. / Goulding, C.W. / Hayes, C.S. / Nhan, D.Q.
History
DepositionMay 8, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 15, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Contact-dependent inhibitor A
C: CdiI (immunity protein)
A: Contact-dependent inhibitor A
D: CdiI (immunity protein)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,5706
Polymers53,3864
Non-polymers1842
Water3,423190
1
B: Contact-dependent inhibitor A
C: CdiI (immunity protein)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,7853
Polymers26,6932
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1810 Å2
ΔGint-13 kcal/mol
Surface area10970 Å2
MethodPISA
2
A: Contact-dependent inhibitor A
D: CdiI (immunity protein)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,7853
Polymers26,6932
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2240 Å2
ΔGint-14 kcal/mol
Surface area10750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.349, 114.410, 114.639
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

#1: Protein Contact-dependent inhibitor A / CdiA-CT (toxin protein)


Mass: 15474.174 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Citrobacter rodentium (bacteria) / Gene: stbD, E2R62_11320 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A482PFX0
#2: Protein CdiI (immunity protein)


Mass: 11218.980 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Citrobacter rodentium (bacteria) / Gene: ROD_29401 / Production host: Escherichia coli (E. coli) / References: UniProt: D2TJN9
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 190 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.44 Å3/Da / Density % sol: 49.52 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1 M Tris, pH 8.5, 0.2 M sodium chloride, 25% PEG3350

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Data collection

DiffractionMean temperature: 110 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 15, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.48→43.05 Å / Num. obs: 18868 / % possible obs: 100 % / Redundancy: 6.6 % / Biso Wilson estimate: 40.54 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.105 / Rpim(I) all: 0.066 / Rrim(I) all: 0.124 / Χ2: 1.02 / Net I/σ(I): 13.1
Reflection shellResolution: 2.48→2.53 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.805 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 2119 / CC1/2: 0.736 / Rpim(I) all: 0.496 / Rrim(I) all: 0.948 / Χ2: 1.02 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 8SSK + AlphaFold model

8ssk


Resolution: 2.48→43.05 Å / SU ML: 0.3127 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.1981
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2367 1885 10 %
Rwork0.1869 16959 -
obs0.1918 18844 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 41.32 Å2
Refinement stepCycle: LAST / Resolution: 2.48→43.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3625 0 12 191 3828
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00233751
X-RAY DIFFRACTIONf_angle_d0.53315080
X-RAY DIFFRACTIONf_chiral_restr0.0495540
X-RAY DIFFRACTIONf_plane_restr0.0043646
X-RAY DIFFRACTIONf_dihedral_angle_d5.4513501
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.48-2.550.36411420.27271283X-RAY DIFFRACTION100
2.55-2.620.331410.23321273X-RAY DIFFRACTION100
2.62-2.710.32331450.23531289X-RAY DIFFRACTION100
2.71-2.80.27321430.22951296X-RAY DIFFRACTION100
2.8-2.920.27271450.23781304X-RAY DIFFRACTION100
2.92-3.050.28011430.22311280X-RAY DIFFRACTION100
3.05-3.210.29251420.22131285X-RAY DIFFRACTION100
3.21-3.410.25361440.20621296X-RAY DIFFRACTION100
3.41-3.670.26041470.18891318X-RAY DIFFRACTION99.86
3.67-4.040.1851420.16051287X-RAY DIFFRACTION99.93
4.04-4.630.18591490.13881338X-RAY DIFFRACTION100
4.63-5.830.20691480.15031327X-RAY DIFFRACTION100
5.83-43.050.18941540.17441383X-RAY DIFFRACTION99.74

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