PDB-8bby: VarB H/L (SLPL/SLPH) complex from C. difficile SlpA (R20291 strain)

ID or keywords:

Entry

Database: PDB / ID: 8bby

Title

VarB H/L (SLPL/SLPH) complex from C. difficile SlpA (R20291 strain)

Components

(S-layer protein) x 2

Keywords

STRUCTURAL PROTEIN / Bacterial surface / S-layer

Function / homology

Low molecular weight S layer protein, N-terminal / Low molecular weight S layer protein, N-terminal, subdomain / Low molecular weight S layer protein N terminal / : / Putative cell wall binding repeat 2 / Cell wall binding domain 2 (CWB2) / outer membrane-bounded periplasmic space / S-layer protein / S-layer protein

Function and homology information

Biological species

Clostridioides difficile R20291 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.9 Å

Authors

Barwinska-Sendra, A. / Salgado, P.S.

Funding support

United Kingdom, 1items

Citation

Journal: Plos Pathog. / Year: 2023
Title: An intact S-layer is advantageous to Clostridioides difficile within the host.
Authors: Ormsby, M.J. / Vaz, F. / Kirk, J.A. / Barwinska-Sendra, A. / Hallam, J.C. / Lanzoni-Mangutchi, P. / Cole, J. / Chaudhuri, R.R. / Salgado, P.S. / Fagan, R.P. / Douce, G.R.

History

Deposition	Oct 14, 2022	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jul 12, 2023	Provider: repository / Type: Initial release
Revision 1.1	Feb 7, 2024	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / diffrn_source / pdbx_initial_refinement_model Item: _diffrn_source.pdbx_synchrotron_site

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8bby.cif.gz	434 KB	Display	PDBx/mmCIF format
PDB format	pdb8bby.ent.gz	354.7 KB	Display	PDB format
PDBx/mmJSON format	8bby.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8bby_validation.pdf.gz	461.4 KB	Display	wwPDB validaton report
Full document	8bby_full_validation.pdf.gz	478.1 KB	Display
Data in XML	8bby_validation.xml.gz	38.7 KB	Display
Data in CIF	8bby_validation.cif.gz	52.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/bb/8bby ftp://data.pdbj.org/pub/pdb/validation_reports/bb/8bby	HTTPS FTP

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Related structure data

Related structure data	7aczS 13957 7acv 7acw 7acx 7acy S: Starting model for refinement
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: S-layer protein

B: S-layer protein

C: S-layer protein

D: S-layer protein

hetero molecules

157 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: S-layer protein

B: S-layer protein

hetero molecules

defined by author&software
Evidence: immunoprecipitation, ELISA assays of WT related proteins Confirmed by gel filtration and electrophoresis of purified samples
78.5 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: S-layer protein

D: S-layer protein

hetero molecules

defined by author&software
Evidence: immunoprecipitation, ELISA assays of WT related proteins Confirmed by gel filtration and electrophoresis of purified samples
78.5 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	108.926, 131.291, 138.269
Angle α, β, γ (deg.)	90.000, 108.780, 90.000
Int Tables number	5
Space group name H-M	C121
Symmetry operation	#1: x,y,z #2: -x,y,-z #3: x+1/2,y+1/2,z #4: -x+1/2,y+1/2,-z

#1: Protein	S-layer protein Mass: 34291.676 Da / Num. of mol.: 2 / Mutation: 249_253insCTTAG in FM2.5 mutant / Source method: isolated from a natural source Source: (natural) Clostridioides difficile R20291 (bacteria) Variant: variant of FM2.5 mutant / References: UniProt: B3GV24
#2: Protein	S-layer protein / S-layer protein SlpA Mass: 44227.180 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) Clostridioides difficile R20291 (bacteria) Variant: variant of FM2.5 mutant / References: UniProt: Q9AEM3
#3: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: 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

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.98 Å³/Da / Density % sol: 58.73 %
Crystal grow	Temperature: 293.15 K / Method: vapor diffusion, sitting drop Details: 0.03 M Magnesium chloride hexahydrate; 0.03 M Calcium chloride dihydrate, 0.12 M Ethyleneglycol, 0.05 M Tris (base); 0.05 M BICINE pH 8.5, 20% v/v Glycerol; 10% w/v PEG 4,000

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.708459 Å
Detector	Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: May 4, 2022
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.708459 Å / Relative weight: 1
Reflection	Resolution: 2.9→36.23 Å / Num. obs: 40129 / % possible obs: 97.82 % / Redundancy: 2 % / B_iso Wilson estimate: 42.81 Å² / CC_1/2: 0.978 / CC star: 0.994 / R_pim(I) all: 0.08566 / Net I/σ(I): 8
Reflection shell	Resolution: 2.9→3 Å / Mean I/σ(I) obs: 2.19 / Num. unique obs: 3584 / CC_1/2: 0.526 / R_pim(I) all: 0.4035 / % possible all: 86.49

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Processing

Software

Name	Version	Classification
PHENIX	1.20.1_4487	refinement
DIALS		data reduction
pointless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 7ACZ

7acz

Resolution: 2.9→36.23 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / Phase error: 32.28 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2869	3839	4.9 %
R_work	0.2438	74523	-
obs	0.2459	40000	97.82 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso max: 149.02 Å² / B_iso mean: 54.32 Å² / B_iso min: 12.88 Å²

Refinement step

Cycle: final / Resolution: 2.9→36.23 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	8352	0	2	32	8386
B_iso mean	-	-	39.87	36.93	-
Num. residues	-	-	-	-	1102

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / R_factor R_free error: 0

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	% reflection obs (%)
2.9-3	0.3147	143	0.3155	3528	86.49
2.94-2.98	0.3768	136	0.3082	2311	85
2.98-3.02	0.3918	117	0.315	2511	89
3.02-3.06	0.3037	132	0.3051	2673	91
3.06-3.1	0.3564	155	0.3164	2571	94
3.1-3.15	0.3232	144	0.2973	2789	97
3.15-3.21	0.3326	161	0.2806	2775	99
3.21-3.26	0.3561	139	0.2797	2850	100
3.26-3.32	0.3274	140	0.2682	2774	99
3.32-3.38	0.3201	171	0.2724	2830	100
3.38-3.45	0.3426	151	0.2628	2777	100
3.45-3.53	0.3111	132	0.2513	2854	100
3.53-3.61	0.3078	155	0.2481	2790	100
3.61-3.7	0.3505	153	0.2521	2849	99
3.7-3.8	0.2556	160	0.23	2720	100
3.8-3.91	0.2882	148	0.235	2869	100
3.91-4.04	0.2721	148	0.2244	2832	100
4.04-4.18	0.338	141	0.2103	2819	100
4.18-4.35	0.198	132	0.1983	2801	100
4.35-4.55	0.2406	136	0.2034	2877	100
4.55-4.79	0.2473	124	0.1932	2845	100
4.79-5.08	0.2451	147	0.2107	2814	100
5.08-5.48	0.2316	155	0.2259	2799	100
5.48-6.02	0.2393	98	0.262	2882	100
6.02-6.89	0.2994	139	0.2585	2801	100
6.89-8.66	0.2333	143	0.2254	2845	99
8.66-36.23	0.2545	139	0.2468	2799	99

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	2.2915	0.3943	0.4295	3.7573	0.2625	1.5234	0.0401	0.3708	-0.685	-0.2048	-0.0843	0.0771	-0.1918	0.0968	0.0669	0.4146	-0.1162	0.0865	0.4177	0.0454	0.8175	-18.4026	-49.9227	-32.2238
2	5.7032	2.1235	2.4398	1.1451	0.7075	1.9575	-0.2569	0.6101	-0.2464	-0.4851	0.487	-0.542	-0.2708	0.261	-0.0979	0.5507	0.0223	0.0395	0.6067	-0.2962	0.8411	-15.1877	-57.4616	-38.9568
3	2.1613	0.0588	0.659	1.8268	-0.6067	1.698	0.1767	0.1826	-0.5747	0.2848	-0.0076	0.2659	0.2192	0.013	-0.2617	0.3082	-0.0188	0.0253	0.4045	0.0195	0.7641	-16.7552	-49.3683	-24.5883
4	2.6122	0.3176	0.3392	3.6769	0.7507	1.5499	0.1399	0.0552	-0.0148	-0.2351	-0.0783	0.6818	-0.017	-0.0553	-0.0617	0.2354	-0.0165	-0.0005	0.3583	-0.0314	0.4851	-21.6991	-33.0186	-24.9271
5	2.4552	0.9769	0.7288	1.0843	0.6662	0.4225	-0.0345	-0.1095	-0.0143	0.1011	-0.0729	0.3543	-0.0269	-0.1153	0.0219	0.2775	-0.0425	0.0917	0.2586	0.0077	0.4683	-6.745	-30.602	-19.3061
6	3.0265	-0.3193	-0.2204	3.0945	-0.975	1.2198	0.0111	-0.0125	-0.0259	0.0827	0.0381	-0.1209	-0.2021	0.374	-0.0212	0.3527	0.0108	0.1463	0.199	-0.07	0.0788	21.1259	-20.797	-14.1619
7	1.7063	0.1073	0.3902	2.7491	0.0309	1.0423	-0.0937	0.0307	-0.1151	0.1336	0.0845	-0.5577	-0.1543	0.1757	0.0414	0.2263	-0.0384	0.0374	0.2543	-0.0288	0.2938	24.6366	-15.0075	-16.2856
8	0.8855	0.5247	-0.187	1.6813	0.0481	0.888	-0.0426	-0.0134	0.034	-0.195	0.1363	0.2178	-0.0197	-0.0461	0.1014	0.1653	-0.0448	-0.1524	0.2686	-0.0216	-0.1131	6.0416	-12.8637	-21.2755
9	1.3895	-0.0669	-0.768	3.2124	-0.083	0.5855	0.0764	0.3058	0.4598	-0.1367	-0.0059	0.6444	0.2013	-0.4151	-0.0713	0.1876	0.0737	-0.0402	0.3755	0.0364	0.2483	-4.5851	-14.8464	-15.4309
10	2.6803	1.3603	0.37	2.4476	-0.7345	1.6654	0.2956	0.5992	0.9215	-0.0164	-0.0742	-0.6111	0.1435	0.1237	-0.1353	0.3705	-0.0557	-0.0127	0.5384	0.092	1.0621	43.1237	-33.4141	-34.1093
11	4.4441	-2.1314	2.5576	1.4026	-0.1877	4.6359	0.0385	-0.4216	0.2446	-0.1298	-0.0527	0.1998	-0.1427	0.0286	-0.0448	0.8268	0.2718	0.0208	0.7362	0.3017	1.0882	37.0817	-21.9643	-35.1005
12	2.7814	0.6329	-0.7063	2.0228	-0.5042	3.7214	0.8863	0.3935	0.7988	0.5398	0.4126	0.3906	-0.1934	0.1154	-0.2648	0.4814	0.0126	0.105	0.5117	0.0579	1.2556	40.2942	-29.0616	-29.9332
13	6.3185	-0.0289	2.5955	1.6659	0.0293	8.3854	0.3358	0.0129	-0.0613	0.084	0.1001	0.0119	-0.1268	0.2638	-0.5357	0.4892	-0.1503	-0.0191	0.2716	0.0584	0.9134	45.2452	-35.7417	-25.0726
14	4.5891	0.4565	2.9946	0.0891	0.3365	2.0811	0.0636	-0.8839	0.0521	0.3155	0.4534	-0.5218	-0.2193	0.7923	-0.0672	0.4787	-0.0382	-0.1901	0.5238	-0.0748	0.5159	59.3817	-48.2391	-12.3609
15	3.3381	0.3001	-0.453	4.1293	0.185	2.6735	-0.2437	-0.0697	0.4653	-0.2192	0.1334	0.0408	0.2096	0.0956	0.1229	0.2985	-0.0447	-0.0292	0.3383	0.015	0.4059	47.5974	-53.0737	-22.2706
16	0.7243	0.8716	0.9222	5.5701	-1.6771	2.9093	0.3366	0.0464	0.6161	-0.9286	-0.2075	-0.6174	0.114	0.5709	0.2057	0.4045	-0.0003	0.1297	0.6165	-0.0662	1.0923	59.15	-48.3928	-30.0863
17	1.1351	1.0969	1.2393	6.574	-0.8758	3.6764	-0.1119	0.2825	-0.0472	-0.2741	0.1172	0.4229	0.1714	-0.4362	0.0134	0.2386	-0.0331	0.0402	0.2937	0.2208	0.871	43.8096	-46.1123	-20.3795
18	2.1618	0.4167	-0.3118	1.1137	-0.3073	0.1745	0.0561	0.0748	-0.0474	0.0235	-0.0843	-0.2194	0.0692	0.1139	0.1465	0.2682	0.0164	0.0247	0.2923	-0.0004	0.4853	33.0218	-54.4371	-17.6094
19	2.4597	-0.3543	-0.5102	3.0967	0.3897	1.2618	-0.1726	-0.0143	-0.1037	0.1871	0.1037	0.3367	0.2666	-0.1653	0.0869	0.2048	-0.0194	-0.0077	0.225	0.0082	0.2526	7.8588	-68.6129	-16.2796
20	2.8872	-0.4739	0.6767	3.2097	-0.123	1.6319	-0.0654	0.0918	-0.1927	-0.1102	0.2096	-0.5726	0.0941	0.2344	-0.0866	0.218	0.017	0.053	0.2176	-0.0471	0.3042	27.2344	-68.2248	-20.4823

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 4 through 29 )	A	4 - 29
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 30 through 68 )	A	30 - 68
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 69 through 265 )	A	69 - 265
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 266 through 316 )	A	266 - 316
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 1 through 76 )	B	1 - 76
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 77 through 106 )	B	77 - 106
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 107 through 269 )	B	107 - 269
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 270 through 386 )	B	270 - 386
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 387 through 416 )	B	387 - 416
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 3 through 43 )	C	3 - 43
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 44 through 72 )	C	44 - 72
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 73 through 244 )	C	73 - 244
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 245 through 254 )	C	245 - 254
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 255 through 264 )	C	255 - 264
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 265 through 287 )	C	265 - 287
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 288 through 306 )	C	288 - 306
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 307 through 316 )	C	307 - 316
18	X-RAY DIFFRACTION	18	chain 'D' and (resid 4 through 92 )	D	4 - 92
19	X-RAY DIFFRACTION	19	chain 'D' and (resid 93 through 280 )	D	93 - 280
20	X-RAY DIFFRACTION	20	chain 'D' and (resid 281 through 415 )	D	281 - 415

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