PDB-8fbe: Crystal structure of OrfX1 from Clostridium botulinum E1

ID or keywords:

Entry

Database: PDB / ID: 8fbe

Title

Crystal structure of OrfX1 from Clostridium botulinum E1

Components

Neurotoxin complex component Orf-X1

Keywords

UNKNOWN FUNCTION / Botulinum neurotoxin

Function / homology

Neurotoxin complex component Orf-X1

Function and homology information

Biological species

Clostridium botulinum E1 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 1.73 Å

Authors

Liu, S. / Gao, L.

Funding support

United States, 1items

Citation

Journal: Febs Lett. / Year: 2023
Title: Crystal structures of OrfX1, OrfX2 and the OrfX1-OrfX3 complex from the orfX gene cluster of botulinum neurotoxin E1.
Authors: Gao, L. / Lam, K.H. / Liu, S. / Przykopanski, A. / Lubke, J. / Qi, R. / Kruger, M. / Nowakowska, M.B. / Selby, K. / Douillard, F.P. / Dorner, M.B. / Perry, K. / Lindstrom, M. / Dorner, B.G. ...

History

Deposition	Nov 29, 2022	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Dec 21, 2022	Provider: repository / Type: Initial release
Revision 1.1	Feb 8, 2023	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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2	Mar 8, 2023	Group: Database references / Category: citation Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3	Oct 23, 2024	Group: Data collection / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature Item: _pdbx_entry_details.has_protein_modification

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8fbe.cif.gz	145.8 KB	Display	PDBx/mmCIF format
PDB format	pdb8fbe.ent.gz	115.3 KB	Display	PDB format
PDBx/mmJSON format	8fbe.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

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

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Related structure data

Related structure data	8fbdC 8fbfC 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: Neurotoxin complex component Orf-X1

B: Neurotoxin complex component Orf-X1

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

1

A: Neurotoxin complex component Orf-X1

defined by author
Evidence: gel filtration
16.8 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Neurotoxin complex component Orf-X1

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

Unit cell

Length a, b, c (Å)	56.602, 56.602, 84.299
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	145
Space group name H-M	P3₂

#1: Protein	Neurotoxin complex component Orf-X1 Mass: 16778.240 Da / Num. of mol.: 2 / Mutation: C31S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Clostridium botulinum E1 (bacteria) / Strain: 'BoNT E Beluga' / Production host: Escherichia coli (E. coli) / References: UniProt: A0A126JJ68
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 238 / 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: 2.32 Å³/Da / Density % sol: 47.06 %
Crystal grow	Temperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 25 % Polyethylene glycol (PEG) 3550 (Hampton Research), 0.2 M ammonium acetate and 0.1 M Bis-tris pH 5.5

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
Detector	Type: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 21, 2015
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97918 Å / Relative weight: 1
Reflection	Resolution: 1.73→19.94 Å / Num. obs: 31471 / % possible obs: 99.8 % / Redundancy: 3.5 % / B_iso Wilson estimate: 23.57 Å² / CC_1/2: 0.999 / Net I/σ(I): 17.3
Reflection shell	Resolution: 1.73→1.76 Å / Num. unique obs: 1762 / CC_1/2: 0.555

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Processing

Software

Name	Version	Classification
PHENIX	1.19.2_4158	refinement
XDS		data reduction
XDS		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

SAD / Resolution: 1.73→19.94 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 23.97 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2165	1523	4.84 %
R_work	0.1721	-	-
obs	0.1743	31471	99.78 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 1.73→19.94 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2319	0	0	238	2557

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	2415
X-RAY DIFFRACTION	f_angle_d	1.08	3248
X-RAY DIFFRACTION	f_dihedral_angle_d	14.845	920
X-RAY DIFFRACTION	f_chiral_restr	0.046	375
X-RAY DIFFRACTION	f_plane_restr	0.004	408

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 (%)
1.73-1.7858	0.3518	150	0.2962	2737	X-RAY DIFFRACTION	100
1.7858-1.8496	0.3351	136	0.2651	2735	X-RAY DIFFRACTION	100
1.8496-1.9236	0.2793	130	0.2249	2721	X-RAY DIFFRACTION	100
1.9236-2.0111	0.2761	126	0.1958	2722	X-RAY DIFFRACTION	100
2.0111-2.117	0.2243	132	0.1873	2759	X-RAY DIFFRACTION	100
2.117-2.2495	0.2359	156	0.1749	2706	X-RAY DIFFRACTION	100
2.2495-2.4229	0.2592	148	0.1748	2702	X-RAY DIFFRACTION	100
2.4229-2.6662	0.2259	154	0.1754	2720	X-RAY DIFFRACTION	100
2.6662-3.0508	0.1999	132	0.1715	2718	X-RAY DIFFRACTION	100
3.0508-3.8392	0.2036	107	0.1535	2752	X-RAY DIFFRACTION	100
3.8392-19.94	0.1704	152	0.1462	2676	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	7.9755	-1.4743	-5.2312	4.7358	0.2026	2.1156	0.2503	-0.6331	0.7326	0.086	-0.2961	0.7165	-0.4432	-0.7649	0.1993	0.2175	0.0013	0.0118	0.3482	-0.0958	0.3617	-17.3783	22.2591	24.4876
2	7.237	-5.7044	-2.3207	2.2598	5.4408	8.1145	-0.0058	0.1921	-0.8703	0.1291	-0.5646	0.7152	0.8536	-0.8241	0.3889	0.2679	-0.0988	0.0849	0.1957	-0.0119	0.3724	-12.7648	4.5602	18.4145
3	2.2043	1.8583	-3.7332	2.3167	-6.697	2.2545	0.1159	0.4703	0.085	0.1333	-0.1239	-0.0436	-0.4054	-0.1979	0.1467	0.3035	-0.0452	-0.0166	0.231	-0.0035	0.1849	-4.1397	25.3757	19.7707
4	8.2496	5.773	-1.0965	6.6951	0.9806	1.3858	-0.1766	0.7154	0.1573	-0.5165	0.2593	-0.2171	-0.3832	0.0864	-0.0903	0.2367	-0.0264	0.0007	0.245	0.0769	0.1769	1.8421	25.1189	11.5723
5	0.8987	0.8968	0.7777	8.3843	0.8134	2.8563	0.0572	-0.3523	-0.5933	0.594	-0.2531	-0.0998	0.2474	-0.1792	0.1819	0.1415	-0.0337	0.0418	0.2576	0.059	0.2741	-9.8077	9.5619	25.6093
6	3.7202	3.8117	1.66	6.6214	1.0401	1.3958	0.1836	-0.4001	-1.0016	0.5261	-0.2349	-0.5497	0.4092	-0.1073	0.0292	0.2486	-0.0347	0.0924	0.2104	0.103	0.4366	-7.7694	0.7604	25.1241
7	4.2511	0.2983	-0.5174	7.0968	-2.4538	6.2516	-0.2852	0.9407	0.1848	-0.6404	0.2744	0.8121	-0.7014	-0.2183	0.0022	0.3701	-0.0831	-0.0954	0.2954	0.0595	0.215	-7.3509	23.6914	7.5035
8	7.2746	0.1275	-2.0887	3.8195	2.4059	8.8467	0.1254	0.4291	0.3267	-0.4614	-0.1671	1.3403	-0.5084	-1.0375	0.0287	0.2169	0.0009	-0.0539	0.3879	-0.0278	0.3886	-19.5745	15.4534	13.3946
9	2.0959	7.359	-5.0902	7.4897	-2.5249	4.1643	-0.1668	0.3675	-0.6711	-0.6824	0.3614	0.0177	1.5367	0.6344	-0.2459	0.6392	-0.0108	-0.1154	0.3739	-0.1037	0.4807	-11.5002	4.5972	5.135
10	4.457	0.7777	0.5757	4.873	-0.8962	6.7134	-0.0712	-0.0609	-0.6432	-0.0188	0.0011	-0.4524	0.3406	0.1442	0.0347	0.1126	-0.0174	0.0314	0.158	0.0142	0.2621	0.6201	10.2025	19.1854
11	2.0344	-2.7167	2.9043	7.3474	-7.2868	8.8899	-0.0426	-1.0644	-0.552	-0.1662	0.2187	0.3933	0.2639	-0.1937	-0.07	0.2383	-0.037	0.084	0.2371	-0.0592	0.3735	-3.6626	6.6469	16.3546
12	4.8717	-0.8303	0.108	5.9697	1.7477	5.2199	-0.019	0.3934	0.2215	-0.7708	-0.1677	0.744	-0.4122	-0.5409	0.2132	0.1865	0.0195	-0.0537	0.2686	0.0211	0.2114	-11.9511	20.6132	12.1883
13	7.6056	-3.1371	0.2116	2.3579	-4.888	9.7134	-0.6118	0.5514	0.6657	0.3834	0.0497	0.1121	-1.1382	0.035	0.4298	0.2985	-0.0165	-0.1126	0.1328	0.0018	0.2926	13.9555	37.0078	25.3873
14	1.9797	1.8212	7.2089	2.0757	-7.3529	7.2028	-0.6008	-0.6928	-0.1281	0.8625	0.009	-0.9263	-0.3818	0.0889	0.7894	0.2562	0.1713	0.061	0.4907	0.1113	0.3797	26.5411	23.3406	30.3681
15	9.3223	5.1874	-3.2289	7.9283	-5.1664	8.6815	-0.038	0.7207	0.7517	-0.0567	0.1351	0.5642	-0.3857	-0.7081	-0.0319	0.1947	0.063	-0.016	0.1484	-0.0554	0.1683	4.6718	29.7229	27.5199
16	9.311	-0.3451	-6.9756	1.7458	-0.4834	9.1415	0.0437	0.4575	-0.0833	0.1378	-0.0323	0.1675	-0.1586	-0.5144	-0.0239	0.1548	-0.0021	-0.0033	0.1129	-0.0196	0.1152	5.9622	25.721	30.1698
17	8.3216	-4.8699	5.7531	5.8001	-1.389	6.268	-0.0478	-0.3097	-0.3934	-0.312	0.1077	-0.3516	0.3202	0.1901	-0.1444	0.1848	0.0727	0.1103	0.3939	0.0942	0.4593	30.1734	18.5704	24.3372
18	6.3401	-0.2403	-4.3014	3.1635	1.1119	6.4382	0.0261	-0.0333	-0.001	0.1376	-0.1115	0.0467	-0.2188	-0.0423	0.1213	0.1151	0.0265	-0.0045	0.0983	0.0301	0.0944	8.2859	26.416	32.1983
19	-0.014	-0.0999	-0.0889	1.0801	0.6144	0.3298	0.4187	-1.0383	0.3892	0.7516	-0.8381	0.3656	-0.5898	0.0832	0.3321	0.7604	-0.5007	-0.1518	1.4443	-0.2085	1.7847	15.2863	43.1128	38.7077
20	8.618	-8.3291	5.9854	2.0938	-8.1948	7.7248	0.0321	-0.4483	0.7783	0.4262	0.0279	-0.5934	-0.1016	0.7506	-0.093	0.2167	-0.0107	-0.0317	0.2744	-0.0151	0.3621	19.4198	33.6258	33.6401
21	4.0639	-0.657	-2.3255	0.9183	0.3668	2.0614	-0.7748	0.1564	0.3811	-0.0166	0.186	-0.0431	0.2905	0.831	0.2132	0.5745	0.0578	-0.3642	0.7945	0.1438	0.8289	24.6919	24.6047	41.4874
22	5.0201	0.4754	-2.973	5.5538	2.2948	7.672	-0.539	0.0686	-0.5377	-0.0645	0.0589	-0.2267	0.6793	0.2117	0.3747	0.1362	0.0067	0.0766	0.1114	0.0091	0.2478	10.1316	19.4695	30.5533
23	5.8376	1.8202	-0.994	4.4273	-3.3117	2.0402	-1.0562	1.1899	-1.5793	-0.4956	-0.149	-0.761	2.6671	0.4385	0.7919	0.5103	0.1056	0.3124	0.4024	0.0648	0.9201	18.0915	11.5219	24.7292
24	9.3943	-1.3963	-2.8508	6.4317	3.681	8.7409	-0.0227	-0.2789	0.1098	0.0517	-0.1693	-0.4914	-0.3612	0.456	0.1978	0.2161	-0.0547	-0.0256	0.1639	0.0905	0.1351	13.02	28.4914	34.4905

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(chain A and resid 1:8)
2	X-RAY DIFFRACTION	2	(chain A and resid 9:22)
3	X-RAY DIFFRACTION	3	(chain A and resid 23:29)
4	X-RAY DIFFRACTION	4	(chain A and resid 30:38)
5	X-RAY DIFFRACTION	5	(chain A and resid 39:49)
6	X-RAY DIFFRACTION	6	(chain A and resid 50:67)
7	X-RAY DIFFRACTION	7	(chain A and resid 68:81)
8	X-RAY DIFFRACTION	8	(chain A and resid 82:92)
9	X-RAY DIFFRACTION	9	(chain A and resid 93:98)
10	X-RAY DIFFRACTION	10	(chain A and resid 99:121)
11	X-RAY DIFFRACTION	11	(chain A and resid 122:131)
12	X-RAY DIFFRACTION	12	(chain A and resid 132:144)
13	X-RAY DIFFRACTION	13	(chain B and resid 1:10)
14	X-RAY DIFFRACTION	14	(chain B and resid 11:20)
15	X-RAY DIFFRACTION	15	(chain B and resid 21:29)
16	X-RAY DIFFRACTION	16	(chain B and resid 30:45)
17	X-RAY DIFFRACTION	17	(chain B and resid 46:60)
18	X-RAY DIFFRACTION	18	(chain B and resid 61:78)
19	X-RAY DIFFRACTION	19	(chain B and resid 79:86)
20	X-RAY DIFFRACTION	20	(chain B and resid 87:91)
21	X-RAY DIFFRACTION	21	(chain B and resid 92:98)
22	X-RAY DIFFRACTION	22	(chain B and resid 99:114)
23	X-RAY DIFFRACTION	23	(chain B and resid 115:124)
24	X-RAY DIFFRACTION	24	(chain B and resid 125:144)

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