PDB-9hb1: Structure of IdeC protease C94S from Streptococcus canis

ID or keywords:

Entry

Database: PDB / ID: 9hb1

Title

Structure of IdeC protease C94S from Streptococcus canis

Components

IgM protease

Keywords

IMMUNE SYSTEM / IgG-degrading protease / IdeS/Mac family cysteine endopeptidase

Function / homology

Ig 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 species

Streptococcus canis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.7 Å

Authors

Acebron, I. / Miguel-Ruano, V. / Hermoso, J.A.

Funding support

Spain, 1items

Citation

Journal: 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

Deposition	Nov 5, 2024	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Oct 1, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9hb1.cif.gz	75.6 KB	Display	PDBx/mmCIF format
PDB format	pdb9hb1.ent.gz		Display	PDB format
PDBx/mmJSON format	9hb1.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9hb1_validation.pdf.gz	442.6 KB	Display	wwPDB validaton report
Full document	9hb1_full_validation.pdf.gz	445.4 KB	Display
Data in XML	9hb1_validation.xml.gz	14.5 KB	Display
Data in CIF	9hb1_validation.cif.gz	18.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/hb/9hb1 ftp://data.pdbj.org/pub/pdb/validation_reports/hb/9hb1	HTTPS FTP

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Related structure data

Related structure data	9hb2C C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: IgM protease

hetero molecules

33.1 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author

Unit cell

Length a, b, c (Å)	70.253, 70.253, 94.884
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	154
Space group name H-M	P3₂21

#1: Protein	IgM protease Mass: 32649.463 Da / Num. of mol.: 1 / Mutation: C94S Source method: isolated from a genetically manipulated source Details: Cys 94 to Ser / Source: (gene. exp.) Streptococcus canis (bacteria) / Gene: ide, FMV2238Y02_23630 / Production host: Escherichia coli M15 (bacteria) / Strain (production host): M15 pREP References: UniProt: A0A3P5YAY8, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases
#2: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO₄
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 32 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N
Has protein modification	N

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.07 Å³/Da / Density % sol: 40.59 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop Details: 30% PEG 3350, 200 mM MgCl2 and 100 mM Tris HCl pH 8.5

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.979 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 5, 2019
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.979 Å / Relative weight: 1
Reflection	Resolution: 2.7→47.44 Å / Num. obs: 7819 / % possible obs: 99.9 % / Redundancy: 9.5 % / CC_1/2: 0.977 / R_pim(I) all: 0.138 / Net I/σ(I): 4.8
Reflection shell	Resolution: 2.7→2.83 Å / Redundancy: 9.5 % / Mean I/σ(I) obs: 1 / Num. unique obs: 1006 / CC_1/2: 0.447 / R_pim(I) all: 0.792 / % possible all: 100

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0425	refinement
XDS		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.7→37.44 Å / Cor.coef. F_o:F_c: 0.942 / Cor.coef. F_o:F_c free: 0.876 / SU B: 22.643 / SU ML: 0.415 / Cross valid method: FREE R-VALUE / ESU R Free: 0.414
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2675	360	4.62 %
R_work	0.2017	7433	-
all	0.205	-	-
obs	-	7793	99.872 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 48.865 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.354 Å²	0.677 Å²	0 Å²
2-	-	1.354 Å²	0 Å²
3-	-	-	-4.391 Å²

Refinement step

Cycle: LAST / Resolution: 2.7→37.44 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2305	0	25	32	2362

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.004	0.012	2383
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	2192
X-RAY DIFFRACTION	r_angle_refined_deg	1.08	1.795	3230
X-RAY DIFFRACTION	r_angle_other_deg	0.393	1.774	5045
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.07	5	293
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	2.303	5	9
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	17.653	10	402
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	14.355	10	116
X-RAY DIFFRACTION	r_chiral_restr	0.05	0.2	351
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.02	2821
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	563
X-RAY DIFFRACTION	r_nbd_refined	0.21	0.2	444
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.211	0.2	2110
X-RAY DIFFRACTION	r_nbtor_refined	0.18	0.2	1148
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.078	0.2	1301
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.158	0.2	72
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.048	0.2	2
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.199	0.2	10
X-RAY DIFFRACTION	r_nbd_other	0.203	0.2	49
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.16	0.2	5
X-RAY DIFFRACTION	r_mcbond_it	2.646	4.865	1169
X-RAY DIFFRACTION	r_mcbond_other	2.644	4.865	1169
X-RAY DIFFRACTION	r_mcangle_it	4.451	8.74	1460
X-RAY DIFFRACTION	r_mcangle_other	4.449	8.743	1461
X-RAY DIFFRACTION	r_scbond_it	2.825	5.101	1214
X-RAY DIFFRACTION	r_scbond_other	2.769	5.071	1195
X-RAY DIFFRACTION	r_scangle_it	4.783	9.26	1769
X-RAY DIFFRACTION	r_scangle_other	4.706	9.207	1740
X-RAY DIFFRACTION	r_lrange_it	6.997	46.893	2584
X-RAY DIFFRACTION	r_lrange_other	6.976	46.926	2581

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	R_factor all	Num. reflection all	Fsc free	Fsc work	% reflection obs (%)	WR_factor R_work
2.7-2.77	0.355	26	0.358	524	0.358	551	0.855	0.88	99.8185	0.349
2.77-2.845	0.359	24	0.34	518	0.341	542	0.897	0.911	100	0.327
2.845-2.927	0.291	18	0.295	534	0.295	552	0.948	0.929	100	0.281
2.927-3.017	0.496	19	0.247	484	0.254	503	0.835	0.95	100	0.223
3.017-3.115	0.261	13	0.265	499	0.265	512	0.958	0.942	100	0.243
3.115-3.224	0.307	28	0.249	467	0.253	495	0.91	0.952	100	0.23
3.224-3.344	0.286	10	0.229	450	0.23	460	0.957	0.963	100	0.209
3.344-3.48	0.232	19	0.214	441	0.215	461	0.951	0.965	99.7831	0.192
3.48-3.633	0.291	23	0.202	408	0.207	431	0.934	0.971	100	0.18
3.633-3.809	0.292	19	0.179	416	0.183	435	0.947	0.977	100	0.157
3.809-4.012	0.31	21	0.185	365	0.191	386	0.954	0.978	100	0.171
4.012-4.253	0.284	14	0.151	365	0.156	381	0.895	0.984	99.4751	0.137
4.253-4.542	0.218	29	0.138	340	0.144	370	0.971	0.986	99.7297	0.127
4.542-4.9	0.184	11	0.135	323	0.137	335	0.977	0.987	99.7015	0.123
4.9-5.359	0.218	17	0.135	302	0.138	319	0.97	0.989	100	0.129
5.359-5.976	0.242	20	0.178	263	0.182	283	0.97	0.982	100	0.161
5.976-6.871	0.302	14	0.197	241	0.203	255	0.984	0.979	100	0.176
6.871-8.345	0.226	23	0.173	201	0.179	224	0.973	0.981	100	0.16
8.345-11.519	0.176	7	0.164	175	0.165	182	0.986	0.984	100	0.157
11.519-37.44	0.251	5	0.259	117	0.259	123	0.782	0.958	99.187	0.266

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