PDB-8bt9: Crystal structure of SlpA domain II (aa 201-310), domain that is ...

ID or keywords:

Entry

Database: PDB / ID: 8bt9

Title

Crystal structure of SlpA domain II (aa 201-310), domain that is involved in the self-assembly and dimerization of the S-layer from Lactobacillus acidophilus

Components

S-layer protein

Keywords

STRUCTURAL PROTEIN / Self-Assembly / Surface Layer / P2 symmetry

Function / homology

Lactobacillus surface layer protein / Surface layer protein A domain / Surface layer protein A domain / structural constituent of cell wall / S-layer / peptidoglycan-based cell wall / extracellular region / NICOTINAMIDE / S-layer protein

Function and homology information

Biological species

Lactobacillus acidophilus (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.1 Å

Authors

Sagmeister, T. / Grininger, C. / Pavkov-Keller, T.

Funding support

Austria, 1items

Citation

Journal: Proc.Natl.Acad.Sci.USA / Year: 2024
Title: The molecular architecture of Lactobacillus S-layer: Assembly and attachment to teichoic acids.
Authors: Sagmeister, T. / Gubensak, N. / Buhlheller, C. / Grininger, C. / Eder, M. / Ðordic, A. / Millan, C. / Medina, A. / Murcia, P.A.S. / Berni, F. / Hynonen, U. / Vejzovic, D. / Damisch, E. ...

History

Deposition	Nov 28, 2022	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Sep 6, 2023	Provider: repository / Type: Initial release
Revision 1.1	Jun 19, 2024	Group: Database references / Category: citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	8bt9.cif.gz	325.5 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	8bt9_validation.pdf.gz	457.8 KB	Display	wwPDB validaton report
Full document	8bt9_full_validation.pdf.gz	460.2 KB	Display
Data in XML	8bt9_validation.xml.gz	15.6 KB	Display
Data in CIF	8bt9_validation.cif.gz	21.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/bt/8bt9 ftp://data.pdbj.org/pub/pdb/validation_reports/bt/8bt9	HTTPS FTP

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Related structure data

Related structure data	7qecC 7qehC 7qfgC 7qfiC 7qfjC 7qfkC 7qflC 7qldC 7qleC 7qlhC 8aluC 8aolC 8q1oC 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: S-layer protein

C: S-layer protein

B: S-layer protein

hetero molecules

38.6 kDa, 3 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
Evidence: light scattering
25.8 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: S-layer protein

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

Unit cell

Length a, b, c (Å)	137.690, 137.690, 51.301
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	154
Space group name H-M	P3₂21
Symmetry operation	#1: x,y,z #2: -y,x-y,z+2/3 #3: -x+y,-x,z+1/3 #4: x-y,-y,-z+1/3 #5: -x,-x+y,-z+2/3 #6: y,x,-z

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	A
3	2	A
4	2	A
5	3	A
6	3	A

NCS domain segments:

Beg auth comp-ID: ASN / Beg label comp-ID: ASN / Auth asym-ID: A / Label asym-ID: A

Dom-ID	Component-ID	Ens-ID	End auth comp-ID	End label comp-ID	Auth seq-ID	Label seq-ID
1	1	1	ASN	ASN	201 - 310	3 - 112
2	1	1	ASN	ASN	201 - 310	3 - 112
3	2	2	LEU	LEU	201 - 311	3 - 113
4	2	2	LEU	LEU	201 - 311	3 - 113
5	3	3	ASN	ASN	201 - 310	3 - 112
6	3	3	ASN	ASN	201 - 310	3 - 112

NCS ensembles :

ID	Details
1	Local NCS retraints between domains: 1 2
2	Local NCS retraints between domains: 3 4
3	Local NCS retraints between domains: 5 6

NCS oper:

ID	Code	Matrix	Vector
1	given	(-0.884398654153, 0.386780571206, 0.261227506726), (0.377732859551, 0.264394832022, 0.887363093449), (0.274147601391, 0.8834569387, -0.379930164786)	16.9868725323, -36.9049626907, 45.6484337169
2	given	(-0.941331457319, -0.323836503061, -0.0950000355119), (-0.330024173444, 0.824445175463, 0.459754497095), (-0.0705629676594, 0.464133678956, -0.882950052751)	8.51848300248, -2.87497229892, 15.5881916138

#1: Protein	S-layer protein / Surface layer protein / SA-protein Mass: 12834.197 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lactobacillus acidophilus (bacteria) / Gene: slpA, LBA0169 / Production host: Escherichia coli (E. coli) / References: UniProt: P35829
#2: Chemical	ChemComp-NCA / NICOTINAMIDE Mass: 122.125 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₆H₆N₂O / Comment: medication*YM
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 153 / 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: 3.65 Å³/Da / Density % sol: 66.26 %
Crystal grow	Temperature: 293.15 K / Method: vapor diffusion, sitting drop Details: Condition: 1.0 M Sodium citrate tribasic dihydrate, 0.1 M MES, pH 6.5 Protein: 10 mg/ml in 150 mM NaCl, 25 mM HEPES, pH 7.0 0.5 ul protein mixed with 0.5 ul condition

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.03323 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 22, 2022
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.03323 Å / Relative weight: 1
Reflection	Resolution: 2.1→47.124 Å / Num. obs: 32853 / % possible obs: 99.97 % / Redundancy: 2 % / B_iso Wilson estimate: 56.71 Å² / CC_1/2: 1 / R_merge(I) obs: 0.01155 / Net I/σ(I): 23.76
Reflection shell	Resolution: 2.1→2.175 Å / Redundancy: 2 % / R_merge(I) obs: 0.4849 / Mean I/σ(I) obs: 1.57 / Num. unique obs: 3272 / CC_1/2: 0.909 / % possible all: 99.97

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0352	refinement
XDS		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.1→47.124 Å / Cor.coef. F_o:F_c: 0.971 / Cor.coef. F_o:F_c free: 0.959 / WR_factor R_free: 0.22 / WR_factor R_work: 0.187 / SU B: 9.472 / SU ML: 0.123 / Average fsc free: 0.9606 / Average fsc work: 0.9665 / Cross valid method: FREE R-VALUE / ESU R: 0.147 / ESU R Free: 0.14
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2221	1696	5.162 %
R_work	0.1892	31157	-
all	0.191	-	-
obs	-	32853	99.976 %

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: 69.669 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.753 Å²	-0.376 Å²	-0 Å²
2-	-	-0.753 Å²	-0 Å²
3-	-	-	2.442 Å²

Refinement step

Cycle: LAST / Resolution: 2.1→47.124 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2495	0	9	153	2657

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.008	0.011	2580
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.016	2316
X-RAY DIFFRACTION	r_angle_refined_deg	1.498	1.647	3533
X-RAY DIFFRACTION	r_angle_other_deg	0.518	1.572	5386
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.587	5	337
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	5.864	5	3
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.926	10	391
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	17.309	10	114
X-RAY DIFFRACTION	r_chiral_restr	0.072	0.2	436
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.02	2955
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	468
X-RAY DIFFRACTION	r_nbd_refined	0.223	0.2	458
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.188	0.2	1987
X-RAY DIFFRACTION	r_nbtor_refined	0.17	0.2	1270
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.08	0.2	1488
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.212	0.2	119
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.215	0.2	49
X-RAY DIFFRACTION	r_nbd_other	0.206	0.2	103
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.188	0.2	12
X-RAY DIFFRACTION	r_mcbond_it	4.806	4.722	1355
X-RAY DIFFRACTION	r_mcbond_other	4.804	4.722	1355
X-RAY DIFFRACTION	r_mcangle_it	6.654	7.026	1690
X-RAY DIFFRACTION	r_mcangle_other	6.652	7.032	1691
X-RAY DIFFRACTION	r_scbond_it	5.68	5.301	1225
X-RAY DIFFRACTION	r_scbond_other	5.678	5.304	1226
X-RAY DIFFRACTION	r_scangle_it	8.016	7.697	1842
X-RAY DIFFRACTION	r_scangle_other	8.014	7.701	1843
X-RAY DIFFRACTION	r_lrange_it	10.821	95.78	10562
X-RAY DIFFRACTION	r_lrange_other	10.806	95.318	10454
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.125	0.05	3090
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.131	0.05	3134
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.135	0.05	2965

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Refine-ID	Type	Rms dev position (Å)	Weight position
1	1	A	X-RAY DIFFRACTION	Local ncs	0.12467	0.05008
1	2	A	X-RAY DIFFRACTION	Local ncs	0.12467	0.05008
2	3	A	X-RAY DIFFRACTION	Local ncs	0.13057	0.05007
2	4	A	X-RAY DIFFRACTION	Local ncs	0.13057	0.05007
3	5	A	X-RAY DIFFRACTION	Local ncs	0.13544	0.05007
3	6	A	X-RAY DIFFRACTION	Local ncs	0.13544	0.05007

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
2.1-2.154	0.272	138	0.303	2282	0.301	2420	0.941	0.926	100	0.281
2.154-2.213	0.266	105	0.278	2225	0.278	2330	0.952	0.941	100	0.252
2.213-2.277	0.313	137	0.267	2137	0.27	2274	0.936	0.949	100	0.237
2.277-2.347	0.253	106	0.242	2134	0.243	2240	0.967	0.961	100	0.209
2.347-2.424	0.27	142	0.231	1976	0.234	2119	0.955	0.967	99.9528	0.194
2.424-2.509	0.279	110	0.217	1964	0.221	2074	0.962	0.973	100	0.183
2.509-2.603	0.198	108	0.22	1912	0.218	2020	0.976	0.974	100	0.183
2.603-2.709	0.254	101	0.199	1846	0.201	1947	0.955	0.977	100	0.172
2.709-2.829	0.239	101	0.207	1763	0.209	1864	0.967	0.974	100	0.184
2.829-2.967	0.292	73	0.233	1683	0.236	1756	0.952	0.967	100	0.208
2.967-3.127	0.257	55	0.217	1664	0.218	1719	0.955	0.971	100	0.203
3.127-3.316	0.256	78	0.228	1510	0.229	1588	0.96	0.971	100	0.218
3.316-3.543	0.234	81	0.224	1429	0.225	1510	0.972	0.974	100	0.216
3.543-3.825	0.226	68	0.204	1343	0.205	1411	0.971	0.976	100	0.203
3.825-4.188	0.215	89	0.168	1225	0.172	1314	0.974	0.983	100	0.173
4.188-4.677	0.156	62	0.147	1120	0.147	1182	0.987	0.988	100	0.159
4.677-5.392	0.143	36	0.143	1014	0.143	1050	0.99	0.988	100	0.152
5.392-6.582	0.294	39	0.165	860	0.169	899	0.953	0.984	100	0.176
6.582-9.219	0.186	42	0.141	670	0.144	713	0.981	0.989	99.8597	0.164
9.219-47.124	0.232	25	0.177	398	0.18	426	0.97	0.975	99.2958	0.208

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	3.2549	-2.3239	-0.0528	1.9899	0.2295	0.1284	-0.0259	0.1392	-0.1047	-0.1605	-0.0904	0.1425	-0.101	-0.0523	0.1163	0.1312	-0.0811	-0.047	0.3641	0.0008	0.3454	13.5671	-64.9071	2.4611
2	1.409	0.2453	-0.8122	0.7731	0.9607	2.4844	0.1474	0.5555	0.2436	0.0646	-0.1897	0.0714	-0.1528	-0.3707	0.0423	0.0585	-0.0644	-0.0288	0.7017	0.2094	0.1929	16.8525	-59.5916	-17.9055
3	1.5745	-0.5102	0.1002	0.5787	0.2133	0.5544	0.1004	-0.1301	0.0915	-0.2255	-0.1882	-0.0339	-0.2536	-0.0676	0.0879	0.188	0.1345	-0.0371	0.2584	-0.0362	0.322	-20.5874	-47.8077	-8.9281

Refinement TLS group

Selection: ALL

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