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- PDB-9pr8: Crystal Structure of the Clostridiodes difficile CspC-CspA hetero... -

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Basic information

Entry
Database: PDB / ID: 9pr8
TitleCrystal Structure of the Clostridiodes difficile CspC-CspA heterodimer.
Components(Germination-specific protease) x 2
KeywordsSIGNALING PROTEIN / Pseudoproteases / heterodimer / signaling proteins
Function / homology
Function and homology information


serine-type endopeptidase activity / proteolysis
Similarity search - Function
Csp protease B, prodomain / Csp protease B prodomain / CspA-like domain / : / Serine proteases, subtilase family, serine active site. / Peptidase S8, subtilisin, Ser-active site / Peptidase S8, subtilisin-related / Serine proteases, subtilase domain profile. / Peptidase S8/S53 domain superfamily / Subtilase family / Peptidase S8/S53 domain
Similarity search - Domain/homology
Germination-specific protease / Germination-specific protease
Similarity search - Component
Biological speciesClostridia (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.35 Å
AuthorsHeldwein, E.E. / Gonzalez-Del Pino, G.L.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)5R01GM108684-08 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)K12GM133314 United States
CitationJournal: To Be Published
Title: The CspC:CspA heterodimer transduces germinant and co-germinant signals during C. difficile spore germination.
Authors: McNellis, M.E. / Gonzalez-Del Pino, G.L. / Serrano-Jimenez, J.A. / Forster, E.R. / Stoica, A.I. / Heldwein, E.E. / Shen, A.
History
DepositionJul 23, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 21, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Germination-specific protease
B: Germination-specific protease
C: Germination-specific protease
D: Germination-specific protease


Theoretical massNumber of molelcules
Total (without water)245,1334
Polymers245,1334
Non-polymers00
Water362
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: assay for oligomerization, Heterodimer was verified by size exclusion chromatography
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4270 Å2
ΔGint-21 kcal/mol
Surface area36410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.143, 105.505, 311.325
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab

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Components

#1: Protein Germination-specific protease


Mass: 60206.156 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridia (bacteria) / Gene: cspBA, CDR20291_2147 / Production host: Escherichia (bacteria) / References: UniProt: A0A9R0BLF4
#2: Protein Germination-specific protease


Mass: 62360.441 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridia (bacteria) / Gene: cspC, CDR20291_2146 / Production host: Escherichia (bacteria) / References: UniProt: A0A9R0BLE1
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H2O
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: 2.38 Å3/Da / Density % sol: 48.39 %
Crystal growTemperature: 300 K / Method: vapor diffusion, sitting drop
Details: 0.2M magnesium chloride, 0.1M Tris-HCl pH 8.5, and 20% w/v PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Dec 9, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 3.35→99.92 Å / Num. obs: 34565 / % possible obs: 99.67 % / Redundancy: 12.3 % / CC1/2: 0.97 / Net I/σ(I): 3.6
Reflection shellResolution: 3.35→3.45 Å / Num. unique obs: 2745 / CC1/2: 0.37 / % possible all: 97.65

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
RAPDdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.35→99.92 Å / SU ML: 0.5336 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.6377
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2782 1733 5.01 %
Rwork0.2462 32832 -
obs0.2478 34565 99.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 81.22 Å2
Refinement stepCycle: LAST / Resolution: 3.35→99.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15997 0 0 2 15999
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011216294
X-RAY DIFFRACTIONf_angle_d1.352722283
X-RAY DIFFRACTIONf_chiral_restr0.06692671
X-RAY DIFFRACTIONf_plane_restr0.01122875
X-RAY DIFFRACTIONf_dihedral_angle_d18.48995592
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.35-3.450.37751450.35342600X-RAY DIFFRACTION97.65
3.45-3.560.36131570.32082689X-RAY DIFFRACTION99.61
3.56-3.690.34911660.3062644X-RAY DIFFRACTION99.72
3.69-3.830.32851440.30732705X-RAY DIFFRACTION99.93
3.83-4.010.32071290.28082718X-RAY DIFFRACTION99.86
4.01-4.220.3131320.25732760X-RAY DIFFRACTION100
4.22-4.490.27251250.23972717X-RAY DIFFRACTION99.96
4.49-4.830.24411350.2232741X-RAY DIFFRACTION99.86
4.83-5.320.27721400.2242752X-RAY DIFFRACTION99.93
5.32-6.090.27341580.24772766X-RAY DIFFRACTION100
6.09-7.670.30811330.24712809X-RAY DIFFRACTION100
7.67-99.920.19441690.18662931X-RAY DIFFRACTION99.58

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