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- PDB-9hb2: Structure of the truncated version of IdeC protease C94S from Str... -

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Basic information

Entry
Database: PDB / ID: 9hb2
TitleStructure of the truncated version of IdeC protease C94S from Streptococcus canis
ComponentsIgM protease
KeywordsIMMUNE SYSTEM / IgG-degrading protease / IdeS/Mac family cysteine endopeptidase
Function / homologyIg protease IdeS / Mac 1 / Papain-like cysteine peptidase superfamily / peptidase activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / proteolysis / IgM protease
Function and homology information
Biological speciesStreptococcus canis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsBatuecas, M.T. / Miguel-Ruano, V. / Hermoso, J.A.
Funding support Spain, 1items
OrganizationGrant numberCountry
Spanish Ministry of Science, Innovation, and UniversitiesPRE2018-085033 Spain
CitationJournal: Infect.Immun. / Year: 2025
Title: Structural and functional characterization of IdeC, a novel IgG-specific protease of Streptococcus canis.
Authors: Walsh, S. / Lapschies, A.M. / Miguel-Ruano, V. / Batuecas, M.T. / Acebron-Avalos, I. / Kohler, T.P. / Hammerschmidt, S. / Eichhorn, I. / Hermoso, J.A. / Fulde, M.
History
DepositionNov 5, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 1, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: IgM protease


Theoretical massNumber of molelcules
Total (without water)32,4751
Polymers32,4751
Non-polymers00
Water2,882160
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area13220 Å2
Unit cell
Length a, b, c (Å)109.379, 109.379, 109.379
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213
Components on special symmetry positions
IDModelComponents
11A-549-

HOH

21A-559-

HOH

31A-560-

HOH

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Components

#1: Protein IgM protease


Mass: 32475.268 Da / Num. of mol.: 1 / Mutation: C94S
Source method: isolated from a genetically manipulated source
Details: Truncated version of IdeC, T48. Single mutation C94S
Source: (gene. exp.) Streptococcus canis (bacteria) / Gene: ide, FMV2238Y02_23630 / Production host: Escherichia coli M15 (bacteria) / Strain (production host): pREP
References: UniProt: A0A3P5YAY8, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 160 / 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: 3.36 Å3/Da / Density % sol: 63.37 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 20% PEG 3350, 200 mM Na/K phosphate, and 100 mM Bis Tris propane pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 12, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.25→48.96 Å / Num. obs: 21011 / % possible obs: 100 % / Redundancy: 12.6 % / CC1/2: 0.997 / Rpim(I) all: 0.059 / Net I/σ(I): 11.3
Reflection shellResolution: 2.25→2.32 Å / Redundancy: 12.7 % / Mean I/σ(I) obs: 1.2 / Num. unique obs: 1916 / CC1/2: 0.431 / Rpim(I) all: 0.706 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.25→48.96 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.944 / SU B: 5.927 / SU ML: 0.14 / Cross valid method: THROUGHOUT / ESU R: 0.201 / ESU R Free: 0.172 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21374 1057 5 %RANDOM
Rwork0.17819 ---
obs0.18004 19931 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.17 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 2.25→48.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2293 0 0 160 2453
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0132350
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172116
X-RAY DIFFRACTIONr_angle_refined_deg1.6061.6353183
X-RAY DIFFRACTIONr_angle_other_deg1.3231.584924
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1595292
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.56123.902123
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.29515397
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.336159
X-RAY DIFFRACTIONr_chiral_restr0.0770.2308
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022658
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02493
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.8384.0381165
X-RAY DIFFRACTIONr_mcbond_other3.8344.0321164
X-RAY DIFFRACTIONr_mcangle_it6.0646.0381455
X-RAY DIFFRACTIONr_mcangle_other6.0626.0451456
X-RAY DIFFRACTIONr_scbond_it4.5474.551185
X-RAY DIFFRACTIONr_scbond_other4.5464.5571186
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.0726.61728
X-RAY DIFFRACTIONr_long_range_B_refined9.31845.7592608
X-RAY DIFFRACTIONr_long_range_B_other9.32945.6932591
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.25→2.309 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.32 85 -
Rwork0.297 1484 -
obs--100 %

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