PDB-8onf: Crystal structure of Bdellovibrio bacteriovorus Bd2439 fibre C-te...

ID or keywords:

Entry

Database: PDB / ID: 8onf

Title

Crystal structure of Bdellovibrio bacteriovorus Bd2439 fibre C-terminal domains with ethylene glycol

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: 1.53 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	Apr 2, 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	Oct 23, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	8onf.cif.gz	309.7 KB	Display	PDBx/mmCIF format
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Validation report

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

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Related structure data

Related structure data	8ojnC 8ok3C 8oksC 8okwC 8ol4C 8omlC 8on4C 8onbC 8oncC 8ondC 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

A: Cell wall surface anchor family protein

B: Cell wall surface anchor family protein

C: Cell wall surface anchor family protein

hetero molecules

91.4 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author

Unit cell

Length a, b, c (Å)	84.368, 161.278, 52.067
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	18
Space group name H-M	P2₁2₁2

Components on special symmetry positions

ID	Model	Components
1	1	C-1433- HOH
2	1	C-1578- HOH

#1: Protein	Cell wall surface anchor family protein Mass: 30335.496 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bdellovibrio bacteriovorus HD100 (bacteria) Gene: Bd2439 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q6MKF5
#2: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C₂H₆O₂ / Feature type: SUBJECT OF INVESTIGATION
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 937 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y
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: 1.95 Å³/Da / Density % sol: 36.8 %
Crystal grow	Temperature: 291.15 K / Method: vapor diffusion, sitting drop Details: 0.1 M Sodium chloride 0.1 M Sodium formate 0.1 M Bis-Tris propane 8.5 6.25 % w/v PEG 3350 6.25%w/v PEG 4000 6.25%w/v PEG 2000 6.25%w/v PEG 5000 MME

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.979 Å
Detector	Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jun 6, 2022
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.979 Å / Relative weight: 1
Reflection	Resolution: 1.53→84.37 Å / Num. obs: 104740 / % possible obs: 96.9 % / Redundancy: 3.3 % / CC_1/2: 0.998 / R_merge(I) obs: 0.062 / R_pim(I) all: 0.037 / R_rim(I) all: 0.073 / Χ²: 0.94 / Net I/σ(I): 11.2 / Num. measured all: 341050
Reflection shell	Resolution: 1.53→1.55 Å / % possible obs: 79.3 % / Redundancy: 2 % / R_merge(I) obs: 0.653 / Num. measured all: 8323 / Num. unique obs: 4168 / CC_1/2: 0.638 / R_pim(I) all: 0.526 / R_rim(I) all: 0.842 / Χ²: 0.65 / Net I/σ(I) obs: 1.1

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Processing

Software

Name	Version	Classification
PHENIX	(1.20.1_4487: ???)	refinement
XDS		data reduction
Aimless		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.53→45.34 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.18 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1851	5230	5 %
R_work	0.1643	-	-
obs	0.1653	104674	96.5 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.53→45.34 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5710	0	28	937	6675

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	5939
X-RAY DIFFRACTION	f_angle_d	0.863	8065
X-RAY DIFFRACTION	f_dihedral_angle_d	7.287	873
X-RAY DIFFRACTION	f_chiral_restr	0.061	926
X-RAY DIFFRACTION	f_plane_restr	0.007	1050

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 (%)
1.53-1.54	0.3272	119	0.3137	2578	X-RAY DIFFRACTION	76
1.54-1.56	0.3291	158	0.2886	2903	X-RAY DIFFRACTION	86
1.56-1.58	0.2685	149	0.2726	2991	X-RAY DIFFRACTION	88
1.58-1.6	0.2803	161	0.2593	3153	X-RAY DIFFRACTION	93
1.6-1.62	0.2797	165	0.2443	3261	X-RAY DIFFRACTION	95
1.62-1.65	0.2695	155	0.2287	3307	X-RAY DIFFRACTION	97
1.65-1.67	0.2434	181	0.2222	3328	X-RAY DIFFRACTION	99
1.67-1.69	0.2702	167	0.2407	3403	X-RAY DIFFRACTION	99
1.69-1.72	0.2594	193	0.2306	3376	X-RAY DIFFRACTION	99
1.72-1.75	0.2481	183	0.2188	3367	X-RAY DIFFRACTION	99
1.75-1.78	0.2336	170	0.1951	3367	X-RAY DIFFRACTION	99
1.78-1.81	0.2281	191	0.1827	3398	X-RAY DIFFRACTION	99
1.81-1.85	0.2187	163	0.1714	3345	X-RAY DIFFRACTION	99
1.85-1.88	0.2069	207	0.1616	3357	X-RAY DIFFRACTION	99
1.88-1.92	0.1987	172	0.1627	3409	X-RAY DIFFRACTION	99
1.92-1.97	0.182	182	0.1543	3373	X-RAY DIFFRACTION	99
1.97-2.02	0.195	206	0.1613	3384	X-RAY DIFFRACTION	99
2.02-2.07	0.1903	186	0.1654	3378	X-RAY DIFFRACTION	99
2.07-2.13	0.1895	165	0.1546	3394	X-RAY DIFFRACTION	99
2.13-2.2	0.1756	171	0.1498	3422	X-RAY DIFFRACTION	99
2.2-2.28	0.1922	174	0.1527	3386	X-RAY DIFFRACTION	99
2.28-2.37	0.1766	184	0.1615	3379	X-RAY DIFFRACTION	99
2.37-2.48	0.2094	173	0.1632	3408	X-RAY DIFFRACTION	98
2.48-2.61	0.206	173	0.1692	3378	X-RAY DIFFRACTION	98
2.61-2.78	0.1785	200	0.1589	3372	X-RAY DIFFRACTION	98
2.78-2.99	0.1776	198	0.1582	3393	X-RAY DIFFRACTION	99
2.99-3.29	0.1556	167	0.1463	3414	X-RAY DIFFRACTION	97
3.29-3.77	0.1489	176	0.1409	3373	X-RAY DIFFRACTION	96
3.77-4.74	0.1291	176	0.1289	3399	X-RAY DIFFRACTION	95
4.74-45.34	0.1643	165	0.1634	3448	X-RAY DIFFRACTION	92

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	0.1148	-0.0414	-0.0059	0.1404	0.0965	0.095	-0.0789	0.163	-0.0132	-0.0281	-0.003	0.141	0.1771	-0.02	-0.0154	0.2639	-0.0086	-0.0369	0.2771	-0.0212	0.1739	-22.2692	15.1099	-13.515
2	0.0441	0.0601	-0.0235	0.1498	0.0365	0.1008	-0.0554	-0.0716	0.0271	-0.0148	0.0315	0.0347	-0.022	-0.0054	-0	0.1586	0.0079	-0.0216	0.1409	-0.0063	0.1714	-13.1901	20.2903	5.7755
3	0.0207	-0.0203	0.0615	0.082	0.0038	0.1049	0.0082	-0.0102	0.0101	-0.0132	-0.0031	-0.0039	-0.0255	-0.0214	-0	0.1438	-0.0038	-0.0093	0.1378	-0.0213	0.1626	22.9774	38.7029	26.9053
4	0.0326	0.0296	-0.0082	0.0205	0.0094	0.0511	-0.0121	0.0905	0.0207	-0.0591	0.0367	0.1179	0.0976	0.0102	-0	0.2478	-0.0042	-0.0278	0.2287	-0.0094	0.2634	-23.9917	4.6058	-7.1637
5	0.58	0.2195	-0.1218	0.0391	0.1167	-0.1396	-0.0312	0.1341	0.0298	-0.0164	0.0247	-0.0283	-0.0085	0.0194	-0.0072	0.151	0.0019	-0.0113	0.1571	-0.0005	0.1379	19.5756	22.8975	4.7675
6	0.0779	0.0381	0.0748	0.0276	0.0051	0.0255	0.0357	0.0512	-0.0576	-0.0564	-0.05	0.1459	0.0095	-0.0595	0	0.1889	0.0049	-0.0188	0.1898	-0.0136	0.1926	-23.9671	6.9725	-2.6257
7	0.4857	-0.1245	-0.0626	0.1089	-0.0617	0.1065	-0.0022	0.1296	-0.1076	0.0236	0.0272	-0.0827	0.0219	-0.0154	-0.0004	0.1604	-0.0158	-0.0001	0.1794	-0.0214	0.1423	-3.9127	8.9522	1.3137
8	0.1856	-0.0339	-0.1125	0.0649	0.0209	0.1801	-0.001	-0.0469	-0.0272	0.0086	-0.0002	-0.0152	0.0581	-0.0187	0	0.1618	-0.0109	-0.0232	0.1376	-0.0031	0.1386	26.1524	16.3391	32.4671

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	{ A\|650-675 }
2	X-RAY DIFFRACTION	2	{ A\|676-770 }
3	X-RAY DIFFRACTION	3	{ A\|771-907 }
4	X-RAY DIFFRACTION	4	{ B\|650-669 }
5	X-RAY DIFFRACTION	5	{ B\|670-907 }
6	X-RAY DIFFRACTION	6	{ C\|652-692 }
7	X-RAY DIFFRACTION	7	{ C693-770 }
8	X-RAY DIFFRACTION	8	{ C\|771-907 }

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