PDB-6mw4: Structure of pseudoprotease CspC from Clostridioides difficile

ID or keywords:

Entry

Database: PDB / ID: 6mw4

Title

Structure of pseudoprotease CspC from Clostridioides difficile

Components

Putative germination-specific protease

Keywords

SIGNALING PROTEIN / CspC / Peptidase S8 family domain in CspA-like proteins

Function / homology

CspA-like domain / Peptidase S8, subtilisin-related / Peptidase S8/S53 domain superfamily /

Subtilase family / Peptidase S8/S53 domain / serine-type endopeptidase activity / Putative germination-specific protease

Function and homology information

Biological species

Peptoclostridium difficile (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 1.55 Å

Authors

Eckenroth, B.E. / Doublie, S.

Funding support

United States, 1items

Citation

Journal: Plos Genet. / Year: 2019
Title: The CspC pseudoprotease regulates germination of Clostridioides difficile spores in response to multiple environmental signals.
Authors: Rohlfing, A.E. / Eckenroth, B.E. / Forster, E.R. / Kevorkian, Y. / Donnelly, M.L. / Benito de la Puebla, H. / Doublie, S. / Shen, A.

History

Deposition	Oct 29, 2018	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jun 26, 2019	Provider: repository / Type: Initial release
Revision 1.1	Jul 24, 2019	Group: Data collection / Database references / Category: citation / citation_author Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2	Jan 1, 2020	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3	Oct 11, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6mw4.cif.gz	233.5 KB	Display	PDBx/mmCIF format
PDB format	pdb6mw4.ent.gz	185.8 KB	Display	PDB format
PDBx/mmJSON format	6mw4.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/mw/6mw4 ftp://data.pdbj.org/pub/pdb/validation_reports/mw/6mw4	HTTPS FTP

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Related structure data

Related structure data	4i0wS S: Starting model for refinement
Similar structure data	6er9-2 4d04-d 5m10-d 4rg3-d 6er9-1 5the-1 3up4-1 5the-2 2ylt-d 4aos-d Search similar-shape structures by Omokage search (details) 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
Related items in Molecule of the Month	#184 - Apr 2015 Glucagon similarity (4) #142 - Oct 2011 PDB Pioneers similarity (4)

Deposited unit

A: Putative germination-specific protease

hetero molecules

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

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	88.651, 155.176, 91.675
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	20
Space group name H-M	C222₁

Components on special symmetry positions

ID	Model	Components
1	1	A-818- HOH
2	1	A-907- HOH

#1: Protein	Putative germination-specific protease Mass: 62360.441 Da / Num. of mol.: 1 / Fragment: CspC Source method: isolated from a genetically manipulated source Source: (gene. exp.) Peptoclostridium difficile (strain R20291) (bacteria) Strain: R20291 / Gene: cspC, CDR20291_2146 / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: C9YNI7
#2: Chemical	ChemComp-SO4 / SULFATE ION / Sulfate Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO₄
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 375 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.53 Å³/Da / Density % sol: 51.34 % / Mosaicity: 0.173 °
Crystal grow	Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.2M MES pH 6.5 with 2.5 M ammonium chloride and 0.5 M guanidinium hydrochloride mixed equal volume with 22 mg/ml protein and equilibrated over 2M sodium chloride

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 23-ID-D / Wavelength: 1.033 Å

Detector

Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 4, 2017 / Details: mirrors

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 1.033 Å / Relative weight: 1

Reflection

Resolution: 1.55→50 Å / Num. obs: 177295 / % possible obs: 99.6 % / Redundancy: 3.4 % / B_iso Wilson estimate: 17.87 Å² / R_merge(I) obs: 0.056 / R_pim(I) all: 0.035 / R_rim(I) all: 0.067 / Χ²: 0.587 / Net I/σ(I): 5.4 / Num. measured all: 595469

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique obs	CC_1/2	R_pim(I) all	R_rim(I) all	Χ²	% possible all
1.55-1.61	3.1	0.595	17407	0.749	0.394	0.716	0.46	97.7
1.61-1.67	3.2	0.485	17741	0.813	0.321	0.585	0.478	99.7
1.67-1.75	3.3	0.356	17757	0.894	0.228	0.425	0.484	99.8
1.75-1.84	3.4	0.248	17740	0.944	0.156	0.294	0.506	99.7
1.84-1.95	3.3	0.16	17765	0.966	0.104	0.192	0.553	99.8
1.95-2.1	3.4	0.106	17792	0.985	0.067	0.126	0.607	99.8
2.1-2.32	3.5	0.076	17725	0.992	0.047	0.09	0.637	99.8
2.32-2.65	3.4	0.056	17777	0.995	0.036	0.067	0.622	99.9
2.65-3.34	3.6	0.042	17779	0.997	0.026	0.05	0.69	99.9
3.34-50	3.5	0.031	17812	0.998	0.019	0.037	0.781	99.9

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Phasing

Phasing

Method:

molecular replacement

Phasing MR

	Highest resolution	Lowest resolution
Rotation	3.86 Å	45.84 Å
Translation	3.86 Å	45.84 Å

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Processing

Software

Name	Version	Classification
PHENIX		refinement
HKL-2000		data reduction
HKL-2000		data scaling
PHASER	2.5.6	phasing
PDB_EXTRACT	3.24	data extraction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4I0W

4i0w

Resolution: 1.55→45.837 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 18.07 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1864	17715	10.03 %
R_work	0.1638	158978	-
obs	0.166	176693	99.6 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso max: 82.48 Å² / B_iso mean: 28.1374 Å² / B_iso min: 9.44 Å²

Refinement step

Cycle: final / Resolution: 1.55→45.837 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4159	0	25	375	4559
B_iso mean	-	-	57.3	36.88	-
Num. residues	-	-	-	-	551

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / R_factor R_free error: 0 / Total num. of bins used: 30

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
1.55-1.5676	0.32	516	0.3096	5240	5756	96
1.5676-1.5861	0.3141	554	0.2972	5229	5783	99
1.5861-1.6054	0.2906	600	0.2756	5296	5896	99
1.6054-1.6257	0.2753	583	0.2544	5256	5839	100
1.6257-1.6471	0.2481	672	0.247	5244	5916	100
1.6471-1.6697	0.2391	627	0.2248	5294	5921	100
1.6697-1.6935	0.232	521	0.2161	5342	5863	100
1.6935-1.7188	0.2296	651	0.2102	5256	5907	100
1.7188-1.7457	0.2209	565	0.1887	5339	5904	100
1.7457-1.7743	0.2067	565	0.1809	5360	5925	100
1.7743-1.8049	0.182	599	0.1706	5294	5893	100
1.8049-1.8377	0.183	528	0.1703	5318	5846	100
1.8377-1.8731	0.2036	564	0.1717	5327	5891	100
1.8731-1.9113	0.1922	687	0.1701	5252	5939	100
1.9113-1.9529	0.1799	561	0.1682	5311	5872	100
1.9529-1.9983	0.1708	545	0.1508	5357	5902	100
1.9983-2.0483	0.1738	681	0.1464	5216	5897	100
2.0483-2.1036	0.152	623	0.1491	5272	5895	100
2.1036-2.1655	0.165	629	0.1432	5263	5892	100
2.1655-2.2354	0.1739	596	0.1464	5353	5949	100
2.2354-2.3153	0.1775	601	0.142	5231	5832	100
2.3153-2.408	0.172	568	0.1516	5376	5944	100
2.408-2.5176	0.1864	669	0.1558	5235	5904	100
2.5176-2.6503	0.1883	599	0.162	5302	5901	100
2.6503-2.8164	0.193	572	0.1616	5305	5877	100
2.8164-3.0338	0.1936	591	0.1686	5335	5926	100
3.0338-3.339	0.192	550	0.164	5341	5891	100
3.339-3.8219	0.1597	543	0.1421	5356	5899	100
3.8219-4.8144	0.1501	518	0.1295	5388	5906	100
4.8144-45.8575	0.1928	637	0.1722	5290	5927	100

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°²)	L12 (°²)	L13 (°²)	L22 (°²)	L23 (°²)	L33 (°²)	S11 (Å °)	S12 (Å °)	S13 (Å °)	S21 (Å °)	S22 (Å °)	S23 (Å °)	S31 (Å °)	S32 (Å °)	S33 (Å °)	T11 (Å²)	T12 (Å²)	T13 (Å²)	T22 (Å²)	T23 (Å²)	T33 (Å²)	Origin x (Å)	Origin y (Å)	Origin z (Å)
1	1.6225	0.5452	-0.2151	1.6522	0.6222	1.5553	0.0873	-0.3092	0.3943	0.1845	0.0117	-0.0272	-0.5511	0.1023	-0.0099	0.2663	0.0021	0.024	0.1483	-0.0589	0.2374	70.6836	60.6844	78.7978
2	1.7341	0.2183	0.4145	1.6183	-0.2692	2.5239	-0.007	0.309	-0.2534	-0.1023	-0.038	-0.0671	0.4313	0.0117	0.0355	0.1437	-0.0007	0.0247	0.1655	-0.0328	0.1525	66.3535	30.9895	58.5137
3	1.1757	0.5546	-0.1174	1.079	0.1364	1.5075	-0.0006	0.013	0.0145	0.0808	0.0103	0.0815	0.0247	-0.1831	-0.0015	0.0931	0.0098	-0.0008	0.136	0.009	0.1197	55.3568	37.9195	71.804
4	1.1585	-0.0556	-0.2901	1.7914	0.1053	1.1721	0.0132	0.0075	0.0976	0.0456	0.0226	0.001	-0.0832	0.0466	-0.0144	0.0726	0.0005	0.0053	0.0896	0.0089	0.0808	68.9547	47.008	69.9576
5	0.536	0.1382	-0.0227	1.2434	0.0633	0.9192	-0.026	0.0523	0.2373	-0.1813	0.0048	-0.2433	-0.2174	0.1187	0.0309	0.1904	-0.0161	0.0251	0.1328	0.0483	0.2117	78.298	60.2818	54.2226
6	1.2908	0.4907	-0.4837	1.46	-0.2496	1.8	0.0437	-0.2189	0.1182	0.2284	0.008	0.0282	-0.4949	0.0811	-0.0649	0.3875	0.0169	-0.0001	0.2597	0.0738	0.3279	74.0606	74.7972	56.3487
7	0.5104	0.3944	-0.3038	0.6125	0.1581	1.1869	-0.1213	-0.1676	-0.0099	0.3476	0.0867	0.0275	-0.4437	0.0871	-0.0108	0.4919	0.0585	0.0057	0.2845	0.0431	0.368	72.8737	74.8606	65.4034
8	0.9191	0.4214	-0.7596	1.4339	-0.4157	1.3242	-0.0363	0.0021	0.1881	0.0291	0.0709	-0.0583	-0.2506	0.102	-0.0143	0.2604	0.0179	-0.0146	0.1465	0.0622	0.2379	75.3414	69.054	54.558
9	1.1362	-0.3556	-0.1271	1.9803	-0.2094	1.3631	0.0137	0.1336	0.1757	-0.0556	-0.0024	-0.1386	-0.1841	0.0131	0.0092	0.1135	-0.0071	0.0137	0.1312	0.0125	0.1265	75.2696	51.7312	51.967
10	1.4579	0.6969	-0.2257	0.8672	0.0732	0.7093	-0.0205	0.2102	0.0909	0.0014	0.0419	0.0561	-0.005	-0.0865	-0.029	0.1222	-0.009	-0.0028	0.176	0.0147	0.1006	63.3764	41.2053	54.6468
11	1.949	-0.4845	-0.0391	3.9524	-0.3378	1.8435	-0.0431	0.0434	-0.1606	0.2012	-0.0035	-0.2919	0.1257	0.1962	0.0334	0.1084	0.0093	-0.0048	0.1371	-0.0044	0.1278	73.3912	33.4402	61.3621
12	0.6823	0.9061	-0.6526	2.0116	-1.3853	0.9576	-0.0349	-0.3543	-1.3372	0.2616	-0.2113	-0.3465	1.0674	0.2982	0.0425	0.4503	0.0226	0.0377	0.2551	0.1452	0.4877	83.7043	29.2303	71.1501
13	0.778	0.4105	-0.313	0.7211	0.127	1.7938	0.0224	0.137	-0.0513	-0.0815	0.0366	-0.0419	0.061	0.1881	-0.0477	0.1397	0.0113	0.003	0.2037	-0.0122	0.1721	83.7298	39.2246	51.2245
14	2.1446	0.2339	0.2835	4.1897	-0.98	2.741	-0.0056	0.1445	-0.5796	0.2412	-0.0502	-0.2952	0.5532	0.4088	0.0529	0.2642	0.0405	-0.0072	0.1871	-0.0213	0.2598	81.6197	29.5108	53.6983
15	0.5202	0.1955	0.7693	2.2248	0.2193	1.1411	-0.1878	0.038	0.158	-0.031	-0.1971	-0.2398	-0.1502	0.1777	0.3335	0.5569	-0.0182	-0.1849	0.536	0.0434	0.8916	93.8614	37.4593	56.8195

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 2 through 70 )	A	2 - 70
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 71 through 105 )	A	71 - 105
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 106 through 188 )	A	106 - 188
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 189 through 268 )	A	189 - 268
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 269 through 294 )	A	269 - 294
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 295 through 335 )	A	295 - 335
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 336 through 380 )	A	336 - 380
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 381 through 411 )	A	381 - 411
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 412 through 455 )	A	412 - 455
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 458 through 483 )	A	458 - 483
11	X-RAY DIFFRACTION	11	chain 'A' and (resid 484 through 503 )	A	484 - 503
12	X-RAY DIFFRACTION	12	chain 'A' and (resid 504 through 514 )	A	504 - 514
13	X-RAY DIFFRACTION	13	chain 'A' and (resid 515 through 540 )	A	515 - 540
14	X-RAY DIFFRACTION	14	chain 'A' and (resid 541 through 555 )	A	541 - 555
15	X-RAY DIFFRACTION	15	chain 'A' and (resid 560 through 565 )	A	560 - 565

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