PDB-9f8f: SLPL/SLPH (H/L) complex C. difficile Opt2472 strain (SLCT2)

ID or keywords:

Entry

Database: PDB / ID: 9f8f

Title

SLPL/SLPH (H/L) complex C. difficile Opt2472 strain (SLCT2)

Components

S-layer protein
SLPH - S-layer protein HMW

Keywords

STRUCTURAL PROTEIN / S-layer / SlpA / C. difficile / SLLP

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 / S-layer protein

Function and homology information

Biological species

Clostridioides difficile (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 3.07 Å

Authors

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

Funding support

United Kingdom, 1items

Citation

Journal: To Be Published
Title: SLPL/SLPH (H/L) complex C. difficile Opt2472 strain
Authors: Barwinska-Sendra, A. / Salgado, P.S.

History

Deposition	May 6, 2024	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Sep 3, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9f8f.cif.gz	620 KB	Display	PDBx/mmCIF format
PDB format	pdb9f8f.ent.gz	422.7 KB	Display	PDB format
PDBx/mmJSON format	9f8f.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9f8f_validation.pdf.gz	449.7 KB	Display	wwPDB validaton report
Full document	9f8f_full_validation.pdf.gz	466 KB	Display
Data in XML	9f8f_validation.xml.gz	51.6 KB	Display
Data in CIF	9f8f_validation.cif.gz	66.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/f8/9f8f ftp://data.pdbj.org/pub/pdb/validation_reports/f8/9f8f	HTTPS FTP

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Related structure data

Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

B: SLPH - S-layer protein HMW

D: SLPH - S-layer protein HMW

C: S-layer protein

A: S-layer protein

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

1

B: SLPH - S-layer protein HMW

A: S-layer protein

defined by author
Evidence: native gel electrophoresis, SLPL:SLPH complex seen in native PAGE and size exclusion chromatography ELISA showing SLPL-SLPH interaction for homologues in CD630 strain
76.9 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

D: SLPH - S-layer protein HMW

C: S-layer protein

defined by author
76.9 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	75.324, 76.480, 78.229
Angle α, β, γ (deg.)	81.800, 78.860, 66.780
Int Tables number	1
Space group name H-M	P1
Space group name Hall	P1
Symmetry operation	#1: x,y,z

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
d_1	ens_1	(chain "A" and (resid 7 through 120 or resid 124 through 316))
d_2	ens_1	(chain "C" and resid 7 through 316)
d_1	ens_2	chain "B"
d_2	ens_2	chain "D"

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
d_1	1	ens_1	PRO	PRO	LYS	LYS	A	D	7 - 120	7 - 120
d_1	2	ens_1	LYS	LYS	LYS	LYS	A	D	124 - 316	124 - 316
d_2	1	ens_1	PRO	PRO	LYS	LYS	C	C	7 - 316	7 - 316
d_1	1	ens_2	THR	THR	MET	MET	B	A	1 - 394	1 - 394
d_2	1	ens_2	THR	THR	MET	MET	D	B	1 - 394	1 - 394

NCS ensembles :

ID
ens_1
ens_2

NCS oper:

ID	Code	Matrix	Vector
1	given	(0.61994072274, -0.737078338385, -0.26905208301), (-0.737007420936, -0.664659173137, 0.122671288618), (-0.269246284607, 0.122244454471, -0.955281493371)	33.1437412401, 60.5149355916, 21.2678675556
2	given	(0.648896411008, -0.689814510931, -0.321075362321), (-0.688104943885, -0.712117824928, 0.139283127554), (-0.324723011169, 0.130553222589, -0.936755476146)	30.5139479682, 61.104544037, 21.8167523844

#1: Protein	SLPH - S-layer protein HMW Mass: 41717.027 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Clostridioides difficile (bacteria) / Strain: Opt2472
#2: Protein	S-layer protein Mass: 35147.086 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Clostridioides difficile (bacteria) / Strain: Opt2472 / References: UniProt: A0A7G4WJU1
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 53 / Source method: isolated from a natural source / Formula: H₂O
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: 2.64 Å³/Da / Density % sol: 53.34 %
Crystal grow	Temperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: 1600 mM Sodium citrate tribasic

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.7085 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 4, 2022
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.7085 Å / Relative weight: 1
Reflection	Resolution: 3.07→35.78 Å / Num. obs: 29132 / % possible obs: 98.9 % / Redundancy: 6.2 % / B_iso Wilson estimate: 13.8 Å² / CC_1/2: 0.813 / Net I/σ(I): 6.2
Reflection shell	Resolution: 3.07→3.18 Å / Redundancy: 6.8 % / Mean I/σ(I) obs: 3.4 / Num. unique obs: 2912 / CC_1/2: 0.417 / % possible all: 99.3

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Processing

Software

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

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 3.07→35.78 Å / SU ML: 0.4386 / Cross valid method: FREE R-VALUE / σ(F): 1.92 / Phase error: 29.1272
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2831	1489	5.13 %
R_work	0.2308	27524	-
obs	0.2335	29013	98.99 %

Solvent computation

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

Displacement parameters

B_iso mean: 21.61 Å²

Refinement step

Cycle: LAST / Resolution: 3.07→35.78 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	10585	0	0	53	10638

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0026	10694
X-RAY DIFFRACTION	f_angle_d	0.4974	14465
X-RAY DIFFRACTION	f_chiral_restr	0.0427	1718
X-RAY DIFFRACTION	f_plane_restr	0.003	1886
X-RAY DIFFRACTION	f_dihedral_angle_d	4.5338	1479

Refine LS restraints NCS

Ens-ID	Dom-ID	Asym-ID	Auth asym-ID	Refine-ID	Type	Rms dev position (Å)
ens_1	d_2	D	A	X-RAY DIFFRACTION	Torsion NCS	1.25676807628
ens_2	d_2	A	B	X-RAY DIFFRACTION	Torsion NCS	0.80499973944

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
3.07-3.17	0.354	137	0.2613	2504	X-RAY DIFFRACTION	99.25
3.17-3.28	0.3637	135	0.2496	2509	X-RAY DIFFRACTION	99.17
3.28-3.41	0.3078	124	0.2514	2512	X-RAY DIFFRACTION	99.4
3.41-3.57	0.3584	128	0.2456	2518	X-RAY DIFFRACTION	99.14
3.57-3.76	0.353	138	0.2894	2489	X-RAY DIFFRACTION	98.02
3.76-3.99	0.2744	139	0.2568	2485	X-RAY DIFFRACTION	98.2
3.99-4.3	0.2287	121	0.2051	2500	X-RAY DIFFRACTION	99.47
4.3-4.73	0.2651	135	0.2111	2472	X-RAY DIFFRACTION	97.46
4.73-5.41	0.2246	161	0.1727	2495	X-RAY DIFFRACTION	99.55
5.41-6.81	0.2305	139	0.2033	2517	X-RAY DIFFRACTION	99.81
6.81-35.78	0.1899	132	0.1971	2523	X-RAY DIFFRACTION	99.55

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	0.0454998726149	0.00609974110041	-0.00287554567842	0.429632102102	-0.0327183786597	0.0152947329223	-0.0364557561194	0.0159020438818	-0.000448460481733	0.00593779425219	-0.045366646009	-0.0463436731324	-0.0783812965619	-0.0474231625354	-0.0216592911476	0.287536078342	-0.176584079281	-0.0658254181865	-0.0438347842164	0.00829628768549	0.117850610546	29.8280297147	41.6694229893	-17.4727717257
2	0.287089899419	0.0761219373225	0.034318070928	0.0726048993301	-0.0270951636145	0.526425135755	-0.0671844917156	-0.0131987511442	-0.0790072363768	0.0575451159016	-0.0990165652674	-0.203256712036	0.0432641124872	0.150959678334	-0.14258003559	0.322896410572	-0.0679604409996	-0.0947933090321	0.0412087766639	-0.101626630264	-0.0933537708562	32.2595869965	10.1749843193	2.56053759585
3	0.111682868426	0.00210327468295	0.147014515708	0.247945320663	-0.104130412217	0.568863000518	-0.0447056841576	-0.0511285732014	-0.0478031340261	-0.121232978647	0.0358763203273	0.0898103338423	0.150702362915	0.0543750920358	-0.00102780040539	0.365629950748	0.0399346012215	0.0480999878319	0.0593530521734	0.0971078168662	0.0408741684204	28.4070439093	-4.27575602175	-0.334947796746
4	0.535695247684	0.164665274582	0.0108922083862	1.4610379781	0.119909766872	0.500555717468	0.079801167913	0.0107869008329	-0.0347101997586	-0.101124435547	0.0253344997257	0.0898855409008	0.058007617332	-0.0708102669626	0.0566149261935	0.316517644068	-0.0853555591537	-0.0694144027726	0.080434675736	-0.0176067057559	0.118469118812	19.0720680682	-1.62407444247	-13.0578128501
5	0.110478223664	0.103416690129	-0.039205841693	0.275910383595	-0.195993363677	0.135675746044	-0.0249962864341	0.123067114572	-0.109407839372	-0.189378548358	0.0375824969332	0.0641243140155	0.0116470732768	0.0490713259888	-0.0182882798422	0.272119640218	-0.0454511937323	-0.0453217326572	0.203700475635	-0.0355671557165	0.0794769208252	21.6716886518	0.313809910225	-24.2531848242
6	0.577114856177	0.0625573078555	-0.0447602384288	0.840687152163	-0.0244878776307	0.569503371554	-0.0267414443017	0.00451805174991	-0.100566667485	-0.0919871386692	0.065519939751	-0.101803972115	0.0364248635346	0.0332346283014	0.021495858012	0.200965516854	-0.00691275630607	0.00476140449033	0.0430902410019	-0.0380679156183	0.121838114072	29.8692094197	16.1358382205	-15.466690343
7	0.237843031083	0.131431674455	0.028592449093	0.111000585404	-0.00828965854346	0.0615508456252	-0.0820082179449	-0.0353145461106	0.0514413478472	-0.0858559645702	-0.0261478954479	-0.123211680099	-0.050263355721	0.000260400921804	-0.0482789401156	0.371188207497	-0.110167832485	-0.089831632886	0.0832279441367	0.0188922882113	-0.0607795141964	26.4439584315	9.18662459172	34.0219562413
8	0.142451805683	0.00230329015083	-0.00950587873234	0.283079506857	0.0622964143626	0.290274561701	0.0470988885684	-0.0109997261313	-0.0396839647636	-0.0659977807821	-0.0337518833413	-0.0527310627003	0.0735002526444	-0.068220056079	0.0248129715294	0.240788661796	-0.175779865521	-0.127875001821	0.0623885668296	-0.145004657143	-0.0397181406935	43.6816699878	31.9267569142	10.2524596725
9	0.279280210137	0.259541676937	0.294264649188	0.307731916309	0.224347600694	0.783558001742	-0.0780744184029	0.108051682755	0.128039125627	0.00591016781919	0.00512555794633	-0.149898589177	-0.15716057789	0.00644206881598	0.03152699893	0.219126285852	-0.12277122418	-0.178377643465	-0.0249168593087	-0.112439716026	0.120054950146	51.9030627589	44.5267608045	12.4292145619
10	0.138468566665	-0.0133667272365	-0.00907430667602	0.136779784259	-0.0145123565387	0.268175111699	0.00784332654465	-0.168338471941	0.193399443819	0.167956111215	0.0676795145486	-0.0402246731184	-0.0990881790004	-0.0767512286828	0.108228934285	0.210763496721	-0.341337722959	-0.392765884161	0.0296091659338	-0.350601835602	-0.360466046941	47.1850970163	36.4446637371	30.6597346661
11	0.686773830613	0.0874061348699	0.0819259747026	0.105266711022	-0.01286489132	0.168471795901	0.0642268476161	-0.116209572315	0.0189892216506	0.0290165328367	0.052179042294	-0.0569529019665	-0.0497253673334	0.0465505412503	0.0185361712189	0.214472804248	-0.0985877571269	-0.184659016595	0.0526738553685	-0.0417963427282	0.108292494551	2.25224397529	-3.11600916828	27.8547913637
12	0.372544440906	0.131587937824	-0.305276169362	0.469794229082	-0.132346058444	0.39574551476	0.00206660239736	0.0851050463781	-0.00308104121118	-0.00534350490232	0.027876129474	0.151713622618	-0.0415940773051	-0.0939149246748	-0.0731083208169	-0.0284866930574	0.0287527683248	0.0320304022105	0.267860456475	0.0638539815244	0.0791030084402	-4.00552155916	-3.66418592325	19.2401541086
13	0.258977710759	-0.00504736204734	-0.209806952172	0.0479459101356	-0.0889395377313	0.278922047113	0.0243541779728	-0.147380348226	0.0502970269256	-0.074629780269	-0.0133167987404	0.0275261204089	-0.100038868816	-0.0588951172831	-0.0183810385072	-0.180460299532	0.130587647441	-0.0652700280403	0.178319993649	0.101456946655	0.163811298854	-12.8926067501	-15.484605581	51.491181821
14	0.391506830566	0.505609550661	0.751160945302	0.710306275894	1.25659057194	3.05237553769	0.00557293637975	-0.0831456903582	-0.21644987043	0.14046941973	0.0580272381766	0.065698737851	0.264919513315	0.0091640936518	-0.0325388253803	0.13112277332	0.0580507182016	-0.0686402168109	0.210093383449	0.0767696010585	0.22903158791	-18.3494384537	-28.6587879662	66.9029403114
15	0.0599173314127	-0.00295405115641	-0.033369476994	0.0828438666029	-0.156500952711	0.209448728892	-0.0616049783012	-0.0993948845135	0.0888977857839	0.0614813479961	0.106343548927	0.0944414494754	-0.164492475036	-0.120998337922	-0.0626345220984	0.0388047472474	0.117402206807	0.0675520951159	0.257437685787	-0.0129352994865	0.126901467635	-4.63755265713	-7.69185271972	48.7471731745
16	0.797449825518	-0.07196140164	-0.106502742142	0.84890234505	0.157902525405	0.769138482289	-0.0495071254309	-0.138892404475	0.0124535193886	0.146228835719	-0.0334308755234	0.0534457258746	-0.09841030457	-0.0876699952854	-0.0326173595403	0.0731635752207	0.0703065919835	0.0755342026689	0.118835657669	-0.0106480309798	0.131200188562	18.2061979358	10.3339933839	38.2503805434
17	0.33841726242	-0.240729303386	0.0560223930709	0.2887460892	-0.0580679988748	0.0476399492619	-0.00829499604346	0.0245252057955	0.0673892442319	-0.00160673318004	-0.0407373611074	-0.0578981067267	-0.0659197568826	-0.0428971808431	-0.0117772322515	0.219890612626	-0.150710153405	-0.0963261840817	0.0340822002055	0.129747785594	0.118556493465	26.0978325654	66.0464101518	-5.70751284139
18	0.531256483838	-0.0275605553409	0.0775540549016	0.0642710021181	-0.215224790245	0.658469070295	-0.0240084255914	-0.0471031685042	-0.00994199659643	0.0627259346141	0.0817961199143	0.0784428698836	-0.00615694934098	-0.0463500840559	-0.0182227718666	0.0886131510253	0.196348769493	0.135099176909	0.0156862403029	-0.128051083905	0.267142325117	19.22688471	70.2941992714	4.2749084399
19	0.111982543808	-0.245940634628	0.0522136205161	0.296472352241	-0.152544605521	0.189471410531	0.134064250487	0.0975048283701	0.202074822644	0.0906695032276	-0.0740934606612	-0.169258340559	-0.0594516974045	0.00525163933916	0.0852246889807	0.320650780155	-0.162224145412	-0.189436961624	0.0481550962339	-0.133967622343	-0.275807845467	22.0702797322	80.9464122763	-19.5242428273
20	0.0652480593391	-0.0401493424604	0.107411268103	0.264088840003	-0.172972813744	0.379262101831	0.0101302552818	0.086015608126	-0.0313218931157	0.308853822754	-0.109515467593	-0.140063165823	0.0927710473584	0.042153505723	0.0208142644899	-0.0922766336182	0.211427163002	-0.060579928869	-0.00255223319931	0.146797242186	0.133023920813	18.1920495112	98.22560924	-31.5334244088
21	0.0646213704058	-0.0986699021686	0.00921920467931	0.533475022371	-0.172032204366	0.0935107825553	-0.00516275491081	0.016647059005	-0.0654444929361	0.0127103800925	-0.0254781387794	0.00207128146442	0.051487836567	-0.0367986483105	-0.046377590219	0.274715869955	-0.0986036256447	0.0429844799769	0.0467656922065	-0.0704160778659	0.0757957834653	11.4100591495	81.8719725028	-20.0226107432
22	0.402697211981	-0.217464542285	-0.342921938177	0.185567235492	0.406209547926	1.04015925755	0.00699962386896	-0.018828854276	0.0631535320307	0.079592604637	0.0340529444328	0.0467998022489	-0.197876351629	-0.0303250377025	-0.00765159833425	0.170786494081	-0.0531826974868	0.0287884678996	0.0840636918377	-0.0284570638886	0.0378402080858	35.8900777483	46.7520315518	-17.4277292527
23	1.12839063263	-0.61128639758	0.110019384713	1.62534833604	-0.0835269689024	0.274148264909	-0.00649158911717	0.0687611036914	-0.029363532058	-0.0820195263142	-0.0453350702213	0.0562347966126	0.00650260287462	-0.0501634391621	-0.0181848753449	0.15142360046	-0.00698610938385	0.00567085847459	0.0787678758211	-0.0116020981858	0.153402655804	18.07310677	44.9632869499	-20.3908657736
24	0.952440146857	-0.406066976346	0.765512329097	0.500861400861	-0.469270412683	1.22782895771	0.0059237296354	0.050750787644	0.0921987145634	0.00430133967279	0.0584149702325	0.0809598429277	-0.0395801347396	-0.0557175707586	-0.0106025150532	-0.00667003173218	-0.0211396293987	0.0661366710769	-0.0268112039276	-0.032340543165	0.106661444931	26.351231761	52.0657188943	-17.2697348669

Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

ID	Refine TLS-ID	Selection details	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	chain 'B' and (resid 1 through 40 )	B	A	1 - 40	1 - 40
2	2	chain 'B' and (resid 41 through 130 )	B	A	41 - 130	41 - 130
3	3	chain 'B' and (resid 131 through 189 )	B	A	131 - 189	131 - 189
4	4	chain 'B' and (resid 190 through 246 )	B	A	190 - 246	190 - 246
5	5	chain 'B' and (resid 247 through 296 )	B	A	247 - 296	247 - 296
6	6	chain 'B' and (resid 297 through 394 )	B	A	297 - 394	297 - 394
7	7	chain 'D' and (resid 1 through 40 )	D	B	1 - 40	1 - 40
8	8	chain 'D' and (resid 41 through 130 )	D	B	41 - 130	41 - 130
9	9	chain 'D' and (resid 131 through 189 )	D	B	131 - 189	131 - 189
10	10	chain 'D' and (resid 190 through 394 )	D	B	190 - 394	190 - 394
11	11	chain 'C' and (resid 7 through 31 )	C	C	7 - 31	1 - 25
12	12	chain 'C' and (resid 32 through 84 )	C	C	32 - 84	26 - 78
13	13	chain 'C' and (resid 85 through 170 )	C	C	85 - 170	79 - 161
14	14	chain 'C' and (resid 171 through 184 )	C	C	171 - 184	162 - 175
15	15	chain 'C' and (resid 185 through 278 )	C	C	185 - 278	176 - 269
16	16	chain 'C' and (resid 279 through 318 )	C	C	279 - 318	270 - 309
17	17	chain 'A' and (resid 7 through 31 )	A	D	7 - 31	1 - 25
18	18	chain 'A' and (resid 32 through 57 )	A	D	32 - 57	26 - 51
19	19	chain 'A' and (resid 58 through 148 )	A	D	58 - 148	52 - 142
20	20	chain 'A' and (resid 149 through 212 )	A	D	149 - 212	143 - 206
21	21	chain 'A' and (resid 213 through 251 )	A	D	213 - 251	207 - 245
22	22	chain 'A' and (resid 252 through 278 )	A	D	252 - 278	246 - 272
23	23	chain 'A' and (resid 279 through 300 )	A	D	279 - 300	273 - 294
24	24	chain 'A' and (resid 301 through 316 )	A	D	301 - 316	295 - 310

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