PDB-8okw: Crystal structure of Bdellovibrio bacteriovorus Bd2734 C-terminal...

ID or keywords:

Entry

Database: PDB / ID: 8okw

Title

Crystal structure of Bdellovibrio bacteriovorus Bd2734 C-terminal domain

Components

Cell wall surface anchor family protein

Keywords

CELL ADHESION / Adhesin / Fibre / TNF / TNF-like

Function / homology

Cell wall surface anchor family protein

Function and homology information

Biological species

Bdellovibrio bacteriovorus HD100 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.84 Å

Authors

caulton, S.G. / Lovering, A.L.

Funding support

United Kingdom, 1items

Citation

Journal: Nat Microbiol / Year: 2024
Title: Bdellovibrio bacteriovorus uses chimeric fibre proteins to recognize and invade a broad range of bacterial hosts.
Authors: Caulton, S.G. / Lambert, C. / Tyson, J. / Radford, P. / Al-Bayati, A. / Greenwood, S. / Banks, E.J. / Clark, C. / Till, R. / Pires, E. / Sockett, R.E. / Lovering, A.L.

History

Deposition	Mar 29, 2023	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Oct 25, 2023	Provider: repository / Type: Initial release
Revision 1.1	Jun 26, 2024	Group: Database references / Category: citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _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
Revision 1.2	Nov 13, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	8okw.cif.gz	193.3 KB	Display	PDBx/mmCIF format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ok/8okw ftp://data.pdbj.org/pub/pdb/validation_reports/ok/8okw	HTTPS FTP

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Related structure data

Related structure data	8ojnC 8ok3C 8oksC 8ol4C 8omlC 8on4C 8onbC 8oncC 8ondC 8onfC C: citing same article (ref.)
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

C: Cell wall surface anchor family protein

A: Cell wall surface anchor family protein

B: Cell wall surface anchor family protein

53.1 kDa, 3 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)	52.161, 87.682, 52.754
Angle α, β, γ (deg.)	90.00, 118.88, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Cell wall surface anchor family protein Mass: 17692.031 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bdellovibrio bacteriovorus HD100 (bacteria) Gene: Bd2734 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q6MJN8
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 504 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 1.99 Å³/Da / Density % sol: 38.2 %
Crystal grow	Temperature: 291.15 K / Method: vapor diffusion, sitting drop / Details: 0.2 M ammonium citrate dibasic, 20 % w/v PEG 3350

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
Detector	Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 6, 2022
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9795 Å / Relative weight: 1
Reflection	Resolution: 1.84→45.67 Å / Num. obs: 23686 / % possible obs: 65.1 % / Redundancy: 3 % / CC_1/2: 0.999 / Net I/σ(I): 20.1
Reflection shell	Resolution: 1.84→2.01 Å / Num. unique obs: 1184 / CC_1/2: 0.961

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Processing

Software

Name	Version	Classification
PHENIX	1.20.1-4487	refinement
autoPROC		data reduction
STARANISO		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.84→45.17 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.31 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1699	1207	5.1 %
R_work	0.1393	-	-
obs	0.141	23679	65.11 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.84→45.17 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3466	0	0	504	3970

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.012
X-RAY DIFFRACTION	f_angle_d	1.195
X-RAY DIFFRACTION	f_dihedral_angle_d	13.68	1246
X-RAY DIFFRACTION	f_chiral_restr	0.074	548
X-RAY DIFFRACTION	f_plane_restr	0.008	614

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 (%)
1.84-1.91	0.3077	15	0.2076	212	X-RAY DIFFRACTION	6
1.91-2	0.2672	49	0.1645	766	X-RAY DIFFRACTION	20
2-2.1	0.1796	54	0.1548	1365	X-RAY DIFFRACTION	35
2.1-2.23	0.2211	112	0.1373	1966	X-RAY DIFFRACTION	52
2.23-2.4	0.2122	110	0.1475	2920	X-RAY DIFFRACTION	75
2.4-2.65	0.2011	151	0.1546	3849	X-RAY DIFFRACTION	99
2.65-3.03	0.1795	244	0.1494	3766	X-RAY DIFFRACTION	100
3.03-3.82	0.1526	219	0.1258	3829	X-RAY DIFFRACTION	99
3.82-45.17	0.1412	253	0.1303	3799	X-RAY DIFFRACTION	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	2.4668	-1.3029	-1.0373	2.9303	-0.8949	1.4861	-0.1202	-0.0122	0.1853	0.1439	-0.0339	-0.1232	-0.0502	0.2185	0.1423	0.0687	-0.0154	-0.0029	0.0449	0.0054	0.0348	17.4168	-7.1703	0.2156
2	0.1352	0.0161	-0.2518	1.5434	-1.9314	2.9352	-0.0008	0.0164	-0.0608	-0.0448	0.0198	0.0403	-0.0303	-0.1298	0.0131	0.0478	-0.0162	-0.0095	0.0303	-0.0003	0.068	-0.8696	-15.8311	0.1495
3	1.0016	0.1706	0.1159	0.3986	-0.1758	0.4177	-0.0234	0.0262	0.0389	-0.0193	0.0502	-0.0227	0.1131	0.0467	-0.0268	0.0677	0.0159	-0.0008	0.0427	-0.0165	0.0577	13.7878	-15.7414	-1.5748
4	1.997	-0.8462	0.6332	1.4013	-0.3893	0.9346	-0.183	-0.1601	0.1183	0.1907	0.0655	-0.0543	-0.0636	0.0844	0.0582	0.0902	0.0286	-0.0749	0.0764	-0.0052	0.0403	15.283	-8.1374	9.8161
5	2.2444	0.3965	-0.7756	1.0634	-0.7368	2.2542	0.0816	0.0857	0.0675	-0.1667	-0.0292	0.1557	-0.0305	-0.2054	-0.0038	0.0986	0.0227	-0.0008	0.0412	-0.0299	0.0852	-6.3253	-8.5302	4.1755
6	3.1203	-0.1793	-0.2401	1.1202	0.2896	1.719	-0.0295	-0.2193	-0.0195	0.0536	0.011	0.1317	-0.03	-0.1295	0.0255	0.0577	-0.007	0.0186	0.0478	-0.0005	0.0474	1.8305	-12.3618	11.8302
7	1.2565	-0.5487	0.0245	1.0784	0.49	1.5359	-0.3274	-0.0695	0.0846	0.1776	0.2445	0.0108	-0.0138	0.1388	0.0386	0.0806	0.0115	-0.0138	0.1037	0.02	0.0495	18.3457	-15.2597	12.0911
8	4.2011	-0.3903	0.0178	0.4141	0.2508	0.1764	-0.1031	-0.3678	-0.1995	0.0132	0.0588	-0.0669	0.0762	0.0808	0.047	0.0632	0.0054	-0.0107	0.0605	0.0175	0.0744	7.3521	-17.8051	7.547
9	3.1734	1.6179	-1.9346	3.0108	-1.8274	4.4949	0.0125	0.1064	0.068	-0.0981	-0.0188	0.2756	-0.0408	-0.3713	-0.0106	0.0573	0.0124	-0.0051	0.072	-0.0099	0.0827	-7.4502	-15.4896	4.3913
10	2.5489	-0.4841	1.2296	1.1038	-0.3763	1.9375	-0.0706	0.0636	0.0951	0.0019	-0.0024	-0.0194	-0.1168	0.1194	0.1033	0.0541	-0.0051	-0.0068	0.0251	0.0137	0.0652	10.3888	-4.7464	0.6852
11	0.6755	0.6046	-0.0088	0.7549	0.5256	1.6326	0.0304	-0.0839	0.0071	-0.0029	-0.0326	0.044	-0.0075	-0.0411	0.033	0.068	0.0038	-0.0232	-0.0009	0.006	0.0678	6.441	16.2791	8.9503
12	1.4571	0.1276	-0.2805	0.8499	-0.0766	0.4028	-0.0409	-0.0184	-0.0353	0.0034	0.03	-0.0021	0.0098	0.0151	0.0125	0.0457	-0.0036	-0.001	0.031	-0.0002	0.0412	8.178	11.735	6.2813
13	4.3595	2.3941	0.9712	4.1819	-0.2889	1.3238	-0.3047	0.3196	-0.0609	-0.2125	0.1799	-0.1193	0.0073	0.1439	0.0713	0.0632	0.0031	-0.0337	0.0883	0.0079	0.0312	18.0235	-8.3561	24.2133
14	0.4128	-0.3906	-0.2473	1.598	0.4545	0.1912	-0.0571	-0.151	-0.0294	0.2257	0.0054	0.0666	0.0352	-0.1166	0.0027	0.0948	0.0327	-0.0051	0.1744	-0.0226	0.0088	-0.9676	-3.76	32.3921
15	1.1272	0.0346	-0.1127	0.8469	-0.2909	0.628	-0.0332	-0.2193	0.0228	0.2097	0.0499	-0.0563	-0.0228	-0.1089	-0.017	0.0741	0.0079	-0.0048	0.0766	-0.0028	0.0378	10.6867	-7.7968	34.0329
16	1.9707	0.3262	0.2609	0.8084	-0.1504	0.7521	-0.1005	-0.0514	0.2105	0.0603	0.0373	0.0089	-0.1437	-0.0916	0.0459	0.0655	0.0064	-0.0165	0.0491	-0.0151	0.0371	8.3642	1.856	25.5761
17	4.0254	-2.1505	-0.5868	4.0504	0.5062	2.4566	0.0632	-0.0132	-0.0581	-0.02	-0.0331	0.1484	-0.039	-0.3389	-0.023	0.1021	-0.0017	-0.0316	0.1141	0.0062	0.0659	-4.5393	-0.9698	18.7642
18	1.4841	0.1355	-0.0196	0.9148	-0.5529	1.2984	-0.207	0.1653	0.0464	0.1573	0.0427	-0.0858	-0.2657	0.1709	0.1159	0.0978	-0.0152	-0.029	0.0396	0.0075	0.0781	18.5166	5.7071	25.7635
19	1.3213	0.0689	0.136	0.8601	-0.1941	0.8965	-0.0415	-0.1096	0.1366	0.0939	0.0339	0.1378	0.0071	-0.1264	0.0108	0.0738	0.0159	0.0087	0.0968	-0.0266	0.0568	-0.0691	1.7299	29.999
20	4.5237	2.3782	-0.8531	2.882	-1.0256	1.7498	-0.1396	0.0715	-0.3349	-0.0732	0.0805	-0.152	0.1918	-0.1142	0.0576	0.0719	0.0147	0.003	0.041	0.0016	0.0509	10.0571	-9.2459	22.5134

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'C' and (resid 693 through 701 )
2	X-RAY DIFFRACTION	2	chain 'C' and (resid 702 through 715 )
3	X-RAY DIFFRACTION	3	chain 'C' and (resid 716 through 751 )
4	X-RAY DIFFRACTION	4	chain 'C' and (resid 752 through 760 )
5	X-RAY DIFFRACTION	5	chain 'C' and (resid 761 through 770 )
6	X-RAY DIFFRACTION	6	chain 'C' and (resid 771 through 794 )
7	X-RAY DIFFRACTION	7	chain 'C' and (resid 795 through 808 )
8	X-RAY DIFFRACTION	8	chain 'C' and (resid 809 through 817 )
9	X-RAY DIFFRACTION	9	chain 'C' and (resid 818 through 827 )
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 828 through 843 )
11	X-RAY DIFFRACTION	11	chain 'A' and (resid 693 through 715 )
12	X-RAY DIFFRACTION	12	chain 'A' and (resid 716 through 843 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 692 through 701 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 702 through 715 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 716 through 742 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 743 through 785 )
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 786 through 794 )
18	X-RAY DIFFRACTION	18	chain 'B' and (resid 795 through 808 )
19	X-RAY DIFFRACTION	19	chain 'B' and (resid 809 through 827 )
20	X-RAY DIFFRACTION	20	chain 'B' and (resid 828 through 843 )

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