PDB-8fbf: Crystal structure of OrfX2 from Clostridium botulinum E1

ID or keywords:

Entry

Database: PDB / ID: 8fbf

Title

Crystal structure of OrfX2 from Clostridium botulinum E1

Components

Neurotoxin complex component Orf-X2

Keywords

UNKNOWN FUNCTION / Botulinum neurotoxin

Function / homology

Clostridium P47 protein / Clostridium P-47 protein / Toxin

Function and homology information

Biological species

Clostridium botulinum E1 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 1.85 Å

Authors

Lam, K.H. / 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

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8fbf.cif.gz	633.5 KB	Display	PDBx/mmCIF format
PDB format	pdb8fbf.ent.gz		Display	PDB format
PDBx/mmJSON format	8fbf.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8fbf_validation.pdf.gz	1.5 MB	Display	wwPDB validaton report
Full document	8fbf_full_validation.pdf.gz	1.5 MB	Display
Data in XML	8fbf_validation.xml.gz	58.3 KB	Display
Data in CIF	8fbf_validation.cif.gz	85.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/fb/8fbf ftp://data.pdbj.org/pub/pdb/validation_reports/fb/8fbf	HTTPS FTP

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Related structure data

Related structure data	8fbdC 8fbeC 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-X2

B: Neurotoxin complex component Orf-X2

hetero molecules

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

1

A: Neurotoxin complex component Orf-X2

hetero molecules

defined by author
Evidence: gel filtration
85.5 kDa, 1 polymers

2

B: Neurotoxin complex component Orf-X2

hetero molecules

defined by author
85.5 kDa, 1 polymers

Unit cell

Length a, b, c (Å)	106.316, 83.192, 108.421
Angle α, β, γ (deg.)	90.00, 105.77, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Neurotoxin complex component Orf-X2 Mass: 85300.055 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Clostridium botulinum E1 (bacteria) / Strain: 'BoNT E Beluga' / Gene: FC839_10770 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A6B4JMW3
#2: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO₄ / Feature type: SUBJECT OF INVESTIGATION
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 848 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	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: 2.74 Å³/Da / Density % sol: 55.16 %
Crystal grow	Temperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 14% PEG3350, 0.2M Lithium Sulfate, and 0.1M Bis-Tris pH 6

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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: 0.9795 Å
Detector	Type: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 19, 2013
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9795 Å / Relative weight: 1
Reflection	Resolution: 1.85→19.89 Å / Num. obs: 154831 / % possible obs: 99.8 % / Redundancy: 6.7 % / CC_1/2: 0.966 / Net I/σ(I): 22.2
Reflection shell	Resolution: 1.85→1.92 Å / Redundancy: 6.2 % / Num. unique obs: 15605 / CC_1/2: 0.892 / % possible all: 99.5

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Processing

Software

Name	Version	Classification
PHENIX	1.15	refinement
XDS		data reduction
XDS		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

SAD / Resolution: 1.85→19.887 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 30.92 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2395	7633	4.94 %
R_work	0.1912	-	-
obs	0.1936	154466	99.64 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.85→19.887 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	11746	0	20	848	12614

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	12121
X-RAY DIFFRACTION	f_angle_d	1.008	16441
X-RAY DIFFRACTION	f_dihedral_angle_d	14.242	4494
X-RAY DIFFRACTION	f_chiral_restr	0.042	1869
X-RAY DIFFRACTION	f_plane_restr	0.004	2096

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 (%)
1.85-1.871	0.3434	231	0.2858	4906	X-RAY DIFFRACTION	100
1.871-1.893	0.3147	265	0.261	4827	X-RAY DIFFRACTION	99
1.893-1.9161	0.3198	253	0.2517	4825	X-RAY DIFFRACTION	100
1.9161-1.9403	0.3192	255	0.2463	4900	X-RAY DIFFRACTION	99
1.9403-1.9658	0.2848	284	0.2301	4837	X-RAY DIFFRACTION	100
1.9658-1.9927	0.2982	265	0.2196	4849	X-RAY DIFFRACTION	100
1.9927-2.0212	0.3023	222	0.22	4914	X-RAY DIFFRACTION	100
2.0212-2.0513	0.3133	238	0.2112	4889	X-RAY DIFFRACTION	100
2.0513-2.0833	0.2502	234	0.2127	4921	X-RAY DIFFRACTION	100
2.0833-2.1174	0.2526	216	0.2011	4883	X-RAY DIFFRACTION	100
2.1174-2.1539	0.2637	273	0.1987	4843	X-RAY DIFFRACTION	100
2.1539-2.193	0.2465	258	0.1952	4914	X-RAY DIFFRACTION	100
2.193-2.2352	0.2768	259	0.19	4865	X-RAY DIFFRACTION	100
2.2352-2.2807	0.2399	235	0.1899	4880	X-RAY DIFFRACTION	100
2.2807-2.3302	0.2648	253	0.1942	4904	X-RAY DIFFRACTION	100
2.3302-2.3844	0.2672	244	0.1953	4901	X-RAY DIFFRACTION	100
2.3844-2.4439	0.2796	243	0.1984	4948	X-RAY DIFFRACTION	100
2.4439-2.5098	0.27	234	0.1973	4881	X-RAY DIFFRACTION	100
2.5098-2.5835	0.246	265	0.2001	4883	X-RAY DIFFRACTION	100
2.5835-2.6667	0.2466	250	0.2067	4880	X-RAY DIFFRACTION	100
2.6667-2.7618	0.2674	259	0.2068	4884	X-RAY DIFFRACTION	100
2.7618-2.8721	0.2724	241	0.2036	4954	X-RAY DIFFRACTION	100
2.8721-3.0024	0.2543	251	0.2097	4901	X-RAY DIFFRACTION	100
3.0024-3.1601	0.2659	260	0.2057	4875	X-RAY DIFFRACTION	100
3.1601-3.3572	0.2438	267	0.2115	4930	X-RAY DIFFRACTION	100
3.3572-3.615	0.2411	277	0.1959	4899	X-RAY DIFFRACTION	100
3.615-3.9761	0.2239	281	0.1762	4907	X-RAY DIFFRACTION	100
3.9761-4.5455	0.1811	263	0.1491	4898	X-RAY DIFFRACTION	99
4.5455-5.7043	0.1782	287	0.1479	4940	X-RAY DIFFRACTION	100
5.7043-19.887	0.1698	270	0.155	4995	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	1.5532	-0.1828	-0.6105	0.2265	-0.2056	3.8008	-0.0134	-0.1916	-0.0811	0.0396	-0.0112	0.0293	0.0357	0.4315	0.014	0.2136	-0.0154	-0.0256	0.2665	0.0103	0.1896	96.0233	46.4038	9.3846
2	5.0797	0.2147	-1.9095	3.5004	-0.7998	6.1471	0.082	-0.364	0.3037	0.2992	-0.1178	-0.1525	-0.5584	0.5274	0.0003	0.3133	-0.0243	-0.0506	0.2949	0.0015	0.1701	95.7508	52.7917	8.5404
3	0.1105	0.12	-0.3706	0.5908	-0.1555	2.8033	-0.0356	0.0317	0.1623	0.0966	-0.0944	0.0035	-0.3646	0.2871	0.1283	0.2249	-0.0488	-0.0252	0.1292	-0.0247	0.2089	90.6581	55.0746	-13.5236
4	5.7848	1.0469	0	5.5435	-0.8999	4.868	-0.257	-0.389	-0.4484	0.3075	0.1015	0.0421	0.0661	-0.9539	0.2297	0.4674	0.1756	0.1084	0.4003	-0.0209	0.2777	68.7153	58.5324	13.3675
5	0.8791	-0.5265	0.091	0.7395	-0.3211	2.6223	-0.0726	-0.0948	0.1071	0.2427	0.0637	0.0109	-0.5481	-0.1243	0.0157	0.2855	0.0207	0.0141	0.1326	-0.0288	0.1856	75.7488	56.6441	-6.015
6	6.6574	0.1168	1.1861	4.3879	4.1188	6.6084	0.0382	-0.2679	-0.7568	0.6928	0.0833	-0.1527	0.5775	0.2906	-0.1333	0.3453	0.0326	-0.0016	0.2969	0.0581	0.1887	79.6401	49.3988	3.6612
7	0.7977	-0.158	-0.1534	0.8857	-0.137	1.9073	0.0272	-0.1122	0.0734	0.2999	0.0047	-0.0152	-0.2659	0.0441	-0.0357	0.2341	0.0014	0.0017	0.1377	-0.0275	0.1749	81.8834	56.4249	-9.1826
8	1.7191	-0.2571	-1.3177	0.6166	1.4224	5.122	0.0054	0.0437	-0.0968	0.0602	-0.023	-0.0845	0.1553	0.1608	0.0137	0.1366	-0.0002	-0.0326	0.1561	0.0198	0.1943	94.3987	50.1244	-31.3065
9	3.2271	-0.8504	-2.9498	0.4939	1.223	3.397	-0.045	-0.1881	-0.0901	-0.0055	0.0036	-0.0196	0.0004	0.1668	0.0503	0.1565	-0.0369	-0.0301	0.2292	0.0428	0.1787	107.2714	50.0227	-47.3699
10	7.0418	-2.4168	0.3388	3.1369	-0.8008	2.1214	0.0246	-0.1413	0.2129	0.2004	0.0008	-0.1873	-0.3176	0.2945	-0.0641	0.1946	-0.0869	0.0039	0.2535	0.0036	0.1712	122.793	54.2572	-55.5945
11	5.5798	-2.642	0.9214	4.182	-0.3932	2.133	-0.0007	-0.2667	0.8072	0.1728	0.0903	-0.2986	-0.5088	0.2447	-0.0894	0.3225	-0.1155	0.0619	0.3992	-0.0356	0.3552	123.1254	61.9274	-54.124
12	2.1213	-0.0918	-1.8944	0.027	0.2793	2.8819	0.0773	0.4588	0.0763	-0.056	-0.0535	0.0407	-0.2381	-0.3789	-0.0282	0.1877	0.0229	-0.0419	0.2363	0.0242	0.1973	91.2379	54.9215	-47.2987
13	1.3659	-0.1114	-0.6255	0.4839	0.5321	4.5243	-0.0207	0.1561	-0.0897	-0.059	0.0229	-0.0094	0.2906	-0.1586	0.002	0.1821	-0.0143	-0.027	0.2174	0.0146	0.2006	149.5321	46.4733	-83.1233
14	4.376	0.131	-3.1889	3.0507	0.6162	6.8313	0.2126	0.3795	0.2536	-0.1931	-0.0297	0.0371	-0.5038	-0.4433	-0.1693	0.2083	-0.0144	-0.0393	0.249	0.0467	0.197	147.9443	52.0991	-80.851
15	2.5168	0.3011	-0.7002	0.8412	-0.26	2.7787	0.0158	0.132	0.1268	-0.0356	0.0755	-0.0845	-0.2024	0.2036	-0.0815	0.1649	-0.0184	-0.012	0.123	0.0085	0.1967	160.6562	57.2112	-57.9024
16	3.5882	1.0016	-2.4854	1.6278	-1.8794	5.0408	0.0571	0.3883	0.0565	-0.1889	0.0572	-0.2576	-0.1736	0.1859	-0.1002	0.2118	-0.0622	0.0532	0.295	0.006	0.2552	170.4049	61.7686	-80.7489
17	2.9245	-0.4058	1.3093	1.845	-0.9705	9.0563	0.0734	0.5015	-0.1983	-0.2711	0.0531	-0.0719	0.5692	0.6167	-0.1767	0.1615	0.0238	0.0028	0.2326	-0.0155	0.1969	171.2091	45.5024	-58.1989
18	0.6393	0.0774	-0.251	0.4405	-0.1887	1.7822	0.0482	0.1703	0.1497	-0.076	0.1018	-0.0063	-0.1135	0.0954	-0.1436	0.1382	-0.0349	0.0009	0.2054	0.0148	0.2369	163.6144	56.2808	-64.8966
19	1.7345	-0.3088	-0.9357	-0.0414	-0.3203	4.9837	-0.0968	-0.0136	-0.0706	0.0535	0.0988	-0.0259	0.3385	-0.0859	0.0292	0.1638	-0.018	-0.0203	0.1025	0.0055	0.2338	151.1634	49.796	-42.266
20	3.0707	0.8498	-2.3084	0.8935	-0.8503	3.246	-0.1159	-0.2347	0.055	0.1199	0.1266	0.0743	0.154	-0.1082	0.0031	0.206	0.0687	0.0016	0.2597	0.0307	0.1689	138.071	49.5381	-26.0231
21	4.0106	1.0977	-0.8702	1.7629	0.4896	1.2436	0.0551	-0.0353	0.2532	0.0368	0.1203	0.0383	-0.1259	-0.3436	-0.2048	0.2927	0.1158	0.017	0.4056	0.0708	0.2442	124.1897	54.9523	-18.495
22	4.0062	1.2892	0.3129	2.5025	0.3325	2.454	-0.0054	0.075	1.009	-0.0916	0.1255	0.2713	-0.5461	-0.6392	-0.1105	0.336	0.1647	0.0828	0.5429	0.1093	0.5439	122.6566	62.3655	-19.5336
23	3.9905	0.1369	-1.7297	0.8682	0.1323	3.2309	-0.1228	-0.8391	0.1447	0.2945	0.1717	-0.0603	-0.054	0.3911	-0.0408	0.2479	0.0785	-0.026	0.4307	-0.04	0.1994	150.5306	52.5261	-18.3063
24	3.5263	-0.7306	-1.924	2.3362	0.376	3.4079	-0.0562	-0.4925	0.3336	0.1671	0.1275	-0.3115	-0.3493	0.6134	-0.0757	0.1947	-0.0382	-0.0361	0.2143	-0.0177	0.2173	162.8879	59.4642	-43.5924

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(chain A and resid 3:101)
2	X-RAY DIFFRACTION	2	(chain A and resid 102:152)
3	X-RAY DIFFRACTION	3	(chain A and resid 153:194)
4	X-RAY DIFFRACTION	4	(chain A and resid 195:214)
5	X-RAY DIFFRACTION	5	(chain A and resid 215:287)
6	X-RAY DIFFRACTION	6	(chain A and resid 288:303)
7	X-RAY DIFFRACTION	7	(chain A and resid 304:396)
8	X-RAY DIFFRACTION	8	(chain A and resid 397:444)
9	X-RAY DIFFRACTION	9	(chain A and resid 445:533)
10	X-RAY DIFFRACTION	10	(chain A and resid 534:572)
11	X-RAY DIFFRACTION	11	(chain A and resid 573:614)
12	X-RAY DIFFRACTION	12	(chain A and resid 615:744)
13	X-RAY DIFFRACTION	13	(chain B and resid 3:101)
14	X-RAY DIFFRACTION	14	(chain B and resid 102:160)
15	X-RAY DIFFRACTION	15	(chain B and resid 161:197)
16	X-RAY DIFFRACTION	16	(chain B and resid 198:259)
17	X-RAY DIFFRACTION	17	(chain B and resid 260:295)
18	X-RAY DIFFRACTION	18	(chain B and resid 296:396)
19	X-RAY DIFFRACTION	19	(chain B and resid 397:444)
20	X-RAY DIFFRACTION	20	(chain B and resid 445:531)
21	X-RAY DIFFRACTION	21	(chain B and resid 532:573)
22	X-RAY DIFFRACTION	22	(chain B and resid 574:614)
23	X-RAY DIFFRACTION	23	(chain B and resid 615:704)
24	X-RAY DIFFRACTION	24	(chain B and resid 705:745)

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Yorodumi