PDB-3cvz: Structural insights into the molecular organization of the S-laye...

ID or keywords:

Entry

Database: PDB / ID: 3cvz

Title

Structural insights into the molecular organization of the S-layer from Clostridium difficile

Components

S-layer protein

Keywords

STRUCTURAL PROTEIN / surface layer protein / PROTEIN BINDING

Function / homology

Function and homology information

outer membrane-bounded periplasmic space / identical protein binding
Similarity search - Function

Biological species

Clostridium difficile (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MAD / Resolution: 2.4 Å

Authors

Albesa-Jove, D. / Fagan, R.

Citation

Journal: Mol.Microbiol. / Year: 2009
Title: Structural insights into the molecular organization of the S-layer from Clostridium difficile
Authors: Fagan, R.P. / Albesa-Jove, D. / Qazi, O. / Svergun, D.I. / Brown, K.A. / Fairweather, N.F.

History

Deposition	Apr 20, 2008	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Mar 17, 2009	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Version format compliance
Revision 1.2	Oct 25, 2017	Group: Refinement description / Category: software
Revision 1.3	Feb 21, 2024	Group: Data collection / Database references / Derived calculations Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3cvz.cif.gz	380.8 KB	Display	PDBx/mmCIF format
PDB format	pdb3cvz.ent.gz	313.9 KB	Display	PDB format
PDBx/mmJSON format	3cvz.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	3cvz_validation.pdf.gz	490.9 KB	Display	wwPDB validaton report
Full document	3cvz_full_validation.pdf.gz	511.9 KB	Display
Data in XML	3cvz_validation.xml.gz	42.2 KB	Display
Data in CIF	3cvz_validation.cif.gz	58.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/cv/3cvz ftp://data.pdbj.org/pub/pdb/validation_reports/cv/3cvz	HTTPS FTP

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Related structure data

Similar structure data	2vix-1 6gu0-d 6gtv-2 2vix-2 4uzg-d 4yvm-1 6gtz-1 4xob-3 39 4z23-d Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#235 - Jul 2019 AMPA Receptor similarity (1) #142 - Oct 2011 PDB Pioneers similarity (1)

Deposited unit

A: S-layer protein

B: S-layer protein

C: S-layer protein

D: S-layer protein

hetero molecules

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

1

A: S-layer protein

hetero molecules

defined by author&software
29.2 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: S-layer protein

defined by author&software
29 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

C: S-layer protein

hetero molecules

defined by author&software
29.1 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

D: S-layer protein

hetero molecules

defined by author&software
29.1 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	107.059, 107.059, 190.617
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	172
Space group name H-M	P6₄

Components on special symmetry positions

ID	Model	Components
1	1	C-353- HOH

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID
1	1
2	1
1	2
2	2

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Selection details
1	1	1	chain C and (resseq 8:249 )
2	1	1	chain A and (resseq 8:249 )
1	1	2	chain D and (resseq 10:61 or resseq 63:120 or resseq 122:238 or resseq 240:249)
2	1	2	chain B and (resseq 10:61 or resseq 63:120 or resseq 122:238 or resseq 240:249)

NCS ensembles :

ID
1
2

#1: Protein	S-layer protein Mass: 29041.291 Da / Num. of mol.: 4 / Fragment: LMW-SLP residues 1-262 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Clostridium difficile (bacteria) / Strain: CD630 / Gene: slpA / Plasmid: pLMW1-262 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta / References: UniProt: Q1JU94, UniProt: Q183M8*PLUS
#2: Chemical	ChemComp-PO4 / PHOSPHATE ION Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO₄
#3: Chemical	ChemComp-GLY / GLYCINE Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₂H₅NO₂
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 386 / 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

ID	Density Matthews (Å³/Da)	Density % sol (%)
1	2.71	54.69
2

Crystal grow

Temperature (K)	Crystal-ID	Method	pH	Details
291	1	vapor diffusion, sitting drop	4	25% PEG 1500, 0.1M SPG buffer, pH 4.0, vapor diffusion, sitting drop, temperature 291K
291	2	vapor diffusion, sitting drop	4.3	20% PEG 1500, 0.1M SPG buffer, pH 4.3, vapor diffusion, sitting drop, temperature 291K

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Data collection

Diffraction

ID	Mean temperature (K)	Crystal-ID
1	100	1
2	100	1

Diffraction source

Source	Site	Beamline	ID	Wavelength (Å)
SYNCHROTRON	SRS	PX10.1	1	1.117
SYNCHROTRON	SRS	PX10.1	2	0.98006, 0.98035, 0.90651

Detector

Type	ID	Detector	Date
MARMOSAIC 225 mm CCD	1	CCD	Jun 3, 2007
MARMOSAIC 225 mm CCD	2	CCD	Oct 6, 2007

Radiation

ID	Monochromator	Protocol	Monochromatic (M) / Laue (L)	Scattering type	Wavelength-ID
1	Si(III)	SINGLE WAVELENGTH	M	x-ray	1
2	Si(III)	MAD	M	x-ray	1

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	1.117	1
2	0.98006	1
3	0.98035	1
4	0.90651	1

Reflection

Redundancy: 9.4 % / Av σ(I) over netI: 6.3 / Number: 385534 / R_merge(I) obs: 0.122 / Χ²: 0.86 / D res high: 2.5 Å / D res low: 100 Å / Num. obs: 41034 / % possible obs: 94.4

Diffraction reflection shell

Highest resolution (Å)	Lowest resolution (Å)	% possible obs (%)	ID	R_merge(I) obs	Chi squared	Redundancy
5.39	100	99.7	1	0.059	0.901	11.3
4.27	5.39	99.9	1	0.095	0.997	11.4
3.73	4.27	100	1	0.107	0.92	11.4
3.39	3.73	95.5	1	0.156	0.892	8.3
3.15	3.39	83.2	1	0.234	0.817	5.1
2.96	3.15		1	0.387	0.735
2.82	2.96		1	0.459	0.741
2.69	2.82		1	0.527	0.869
2.59	2.69		1	0.562	0.773
2.5	2.59		1	0.625	0.741

Reflection

Resolution: 2.13→100 Å / Num. obs: 68870 / % possible obs: 99.8 % / Redundancy: 17.8 % / R_merge(I) obs: 0.087 / Net I/σ(I): 9.4

Reflection shell

Resolution (Å)	Redundancy (%)	% possible all	R_merge(I) obs
2.13-2.21	10.1	99.7
2.21-2.29	11.3	99	0.83
2.29-2.4	12.8	99.6	0.656
2.4-2.53	14.2	99.6	0.437
2.53-2.68	19.3	100	0.417
2.68-2.89	22.7	100	0.279
2.89-3.18	23.1	100	0.151
3.18-3.64	23	100	0.089
3.64-4.59	22.4	100	0.071
4.59-50	19.3	99.7	0.045

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Phasing

Phasing	Method: MAD

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Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
SHARP		phasing
PHENIX		refinement
PDB_EXTRACT	3.005	data extraction
MAR345		data collection

Refinement

Method to determine structure:

MAD / Resolution: 2.4→46.358 Å / SU ML: 0.41 / σ(F): 1.34 / Phase error: 39.07 / Stereochemistry target values: MLHL

	R_factor	Num. reflection	% reflection
R_free	0.294	1395	2.92 %
R_work	0.2309	-	-
obs	0.2328	47747	99 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 54.709 Å² / k_sol: 0.3 e/Å³

Displacement parameters

B_iso mean: 80.39 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	11.323 Å²	-0 Å²	0 Å²
2-	-	11.323 Å²	0 Å²
3-	-	-	-22.646 Å²

Refinement step

Cycle: LAST / Resolution: 2.4→46.358 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7250	0	5	386	7641

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.01	7319
X-RAY DIFFRACTION	f_angle_d	1.23	9883
X-RAY DIFFRACTION	f_dihedral_angle_d	16.934	2636
X-RAY DIFFRACTION	f_chiral_restr	0.073	1188
X-RAY DIFFRACTION	f_plane_restr	0.004	1273

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Number	Refine-ID	Type	Rms dev position (Å)
1	1	C	1796	X-RAY DIFFRACTION	POSITIONAL
1	2	A	1796	X-RAY DIFFRACTION	POSITIONAL	0.057
2	1	D	1750	X-RAY DIFFRACTION	POSITIONAL
2	2	B	1750	X-RAY DIFFRACTION	POSITIONAL	0.048

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 (%)
2.4-2.4858	0.3469	142	0.28	4609	X-RAY DIFFRACTION	99
2.4858-2.5853	0.3464	145	0.262	4597	X-RAY DIFFRACTION	99
2.5853-2.703	0.3588	139	0.2655	4645	X-RAY DIFFRACTION	99
2.703-2.8455	0.3835	136	0.2675	4639	X-RAY DIFFRACTION	99
2.8455-3.0237	0.3047	135	0.2682	4648	X-RAY DIFFRACTION	99
3.0237-3.2571	0.3534	143	0.2493	4655	X-RAY DIFFRACTION	99
3.2571-3.5848	0.3413	141	0.2392	4654	X-RAY DIFFRACTION	99
3.5848-4.1032	0.2709	137	0.2185	4608	X-RAY DIFFRACTION	98
4.1032-5.1686	0.2599	141	0.1968	4612	X-RAY DIFFRACTION	99
5.1686-46.3665	0.2313	136	0.194	4685	X-RAY DIFFRACTION	99

Refinement TLS params.

Refine-ID: X-RAY DIFFRACTION

ID	Method	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	refined	0.1584	-0.1268	-0.0446	0.0271	-0.0254	-0.0096	0.0102	-0.0328	0.0221	-0.0017	0.0268	-0.0119	0.0105	-0.0044	-0.0016	0.8106	0.0288	-0.0255	0.7704	0.0111	0.8307	-14.9178	-23.6304	-40.5175
2		0.5199	0.3108	0.1361	0.0638	-0.0104	1.0992	0.1786	0.166	0.2414	0.0173	0.1775	0.0578	-0.6865	-0.006	-0.1676	0.2662	0.0455	0.2556	0.078	0.0487	0.0503
3		0.2644	-0.1134	0.0037	0.2839	0.0077	0.0081	-0.1483	-0.1985	-0.1159	0.2039	0.1592	-0.0431	-0.0112	0.0705	0.2034	0.2047	0.2185	0.0864	0.1584	0.0659	0.0966
4		0.2749	-0.0453	-0.0669	0.2443	-0.0051	0.1788	-0.1884	-0.0799	-0.1622	0.0771	0.112	-0.0284	0.1756	0.0874	0.2708	0.409	0.1382	0.1848	0.0469	0.038	0.1024
5		0.0561	-0.0187	-0.0502	0.0448	-0.0299	0.1032	0.0883	-0.018	0.0563	0.039	0.0388	0.006	-0.0625	-0.0352	-0.0328	0.2837	0.2385	0.149	0.2063	0.1035	0.2343
6		-0.0425	-0.0883	-0.0436	-0.0326	-0.0048	0.0284	-0.0018	-0.0043	0.0219	0.0079	-0.0358	0.0233	-0.0195	-0.0294	0.0027	1.1709	-0.0633	0.1658	1.1098	-0.0775	1.2973
7		-0.0802	-0.1184	0.0903	-0.0407	0.0561	0.0132	0.1874	-0.3092	0.294	0.0012	0.2289	-0.2439	-0.3146	0.0733	-0.1003	0.4666	-0.1942	0.1534	0.9831	-0.081	0.3152
8		0.0608	0.0209	0.0058	-0.0187	-0.0092	0.0348	-0.1699	0.0102	0.0922	0.0765	-0.117	-0.0804	-0.0008	-0.0126	0.0627	0.9868	0.0268	0.167	1.1493	-0.2836	0.7135
9		0.4837	0.1151	-0.0074	0.2738	-0.1922	0.2538	-0.0227	-0.3229	-0.0931	-0.2782	0.143	-0.0069	-0.2948	0.2139	-0.0552	0.2784	-0.0724	0.034	0.3514	0.0073	0.0536
10		-0.0243	-0.0177	-0.0424	0.0133	0.0252	0.0652	0.0069	-0.0339	0.1045	0.0036	-0.0042	0.0519	-0.0911	-0.028	-0.0072	0.7319	-0.054	0.1569	0.8854	-0.2397	0.7635
11		0.0285	0.003	-0.0011	0.0472	0.0097	0.0057	-0.0035	0.0086	0.0738	0.0002	0.0049	0.0388	-0.0093	0.0011	-0.0079	0.9746	0.0016	-0.0814	0.9893	0.076	1.1919
12		-0.101	-0.1297	0.0119	0.8396	0.0887	0.2367	0.1799	0.1364	0.0751	-0.3126	0.3171	0.5897	-0.2388	-0.6839	-0.1264	0.5582	-0.1355	0.0308	0.5856	0.3008	0.35
13		0.0034	0.0074	-0.003	-0.0233	0.0018	0.0384	0.0018	-0.0007	0.0048	0.0138	0.0144	0.0227	-0.0228	0.0015	-0.0053	1.099	0.0207	-0.2434	1.1256	0.0986	1.2804
14		0.5688	0.3246	-0.1589	0.2947	-0.0364	0.1953	0.0677	-0.0057	0.0507	-0.1523	0.0975	-0.0917	-0.0658	-0.0785	0.9631	-0.2353	-0.177	0.0782	-0.14	0.1462	-0.08
15		0.647	0.6877	-0.479	0.5815	0.8548	-0.1721	-0.1847	0.384	0.2025	-0.1294	0.2331	0.3708	-0.2692	-0.2443	-0.1472	-0.0652	-0.1066	-0.0387	0.1634	0.1284	0.1727
16		0.0152	0.0373	0.007	0.0881	0.0207	-0.0061	0.0105	0.0144	-0.0074	-0.0143	-0.0019	0.0005	0.0002	-0.0008	-0.0006	0.6077	-0.1436	0.3097	0.7086	-0.1679	0.6658
17		-0.081	-0.2688	-0.1137	0.5028	0.1681	1.174	0.1621	0.0201	0.1417	-0.1053	0.2031	-0.3198	-0.1176	0.521	-0.2445	0.2825	0.1675	0.1212	0.1966	-0.1722	0.0669
18		0.248	-0.2357	-0.1274	0.3365	-0.0192	0.1374	-0.1464	0.0124	-0.0926	0.0436	-0.0129	0.0656	0.0013	-0.0235	-0.1263	0.0561	0.1003	-0.0252	-0.0376	-0.0152	0.1003
19		0.1567	-0.0042	0.0123	0.0057	-0.0295	-0.085	-0.0194	-0.0025	-0.211	0.1038	0.0809	0.0165	0.1203	0.0851	-0.1116	0.2031	0.2501	-0.0357	0.0529	-0.0366	0.0983
20		0.0792	0.0201	-0.0129	0.0345	-0.0208	-0.0178	-0.0165	-0.025	0.0346	-0.0785	0.1005	-0.0229	0.0444	0.0645	-0.0017	0.6181	0.2384	0.1383	0.6294	-0.0796	0.3687

Refinement TLS group

Selection details: chain D and resid 233:249)

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