PDB-6bvd: Structure of Botulinum Neurotoxin Serotype HA Light Chain

ID or keywords:

Entry

Database: PDB / ID: 6bvd

Title

Structure of Botulinum Neurotoxin Serotype HA Light Chain

Components

Light Chain

Keywords

TOXIN / Metalloendopeptidase / Proteolysis

Function / homology

Function and homology information

negative regulation of neurotransmitter secretion / metalloendopeptidase activity / zinc ion binding
Similarity search - Function

Biological species

Clostridium botulinum (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.09 Å

Authors

Jin, R. / Lam, K.

Funding support

United States, 1items

Citation

Journal: Pathog Dis / Year: 2018
Title: Structural and biochemical characterization of the protease domain of the mosaic botulinum neurotoxin type HA.
Authors: Lam, K.H. / Sikorra, S. / Weisemann, J. / Maatsch, H. / Perry, K. / Rummel, A. / Binz, T. / Jin, R.

History

Deposition	Dec 12, 2017	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	May 9, 2018	Provider: repository / Type: Initial release
Revision 1.1	May 30, 2018	Group: Data collection / Database references / Category: citation / Item: _citation.journal_volume
Revision 1.2	Feb 20, 2019	Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3	Dec 18, 2019	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4	Oct 4, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	6bvd.cif.gz	363.8 KB	Display	PDBx/mmCIF format
PDB format	pdb6bvd.ent.gz	295.8 KB	Display	PDB format
PDBx/mmJSON format	6bvd.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	6bvd_validation.pdf.gz	446.7 KB	Display	wwPDB validaton report
Full document	6bvd_full_validation.pdf.gz	452.7 KB	Display
Data in XML	6bvd_validation.xml.gz	36.4 KB	Display
Data in CIF	6bvd_validation.cif.gz	54 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/bv/6bvd ftp://data.pdbj.org/pub/pdb/validation_reports/bv/6bvd	HTTPS FTP

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Related structure data

Related structure data	2a8aS S: Starting model for refinement
Similar structure data	2e5v-d 4kqb-d 6eo4-d 3l6q-d 3hyx-5 6g60-4 7nqx-d 3hyv-4 6arx-d Search similar-shape structures by Omokage search (details) 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: Light Chain

B: Light Chain

hetero molecules

99.7 kDa, 2 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)	76.249, 160.745, 219.099
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	20
Space group name H-M	C222₁

#1: Protein	Light Chain Mass: 49636.078 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Clostridium botulinum (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A384E125*PLUS
#2: Chemical	ChemComp-CA / CALCIUM ION Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical	ChemComp-ACT / ACETATE ION Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂H₃O₂
#4: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 584 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 3.38 Å³/Da / Density % sol: 63.62 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 100 mM calcium acetate, 100 mM sodium cacodylate, 4% PEG 8000

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-E / Wavelength: 0.97918 Å
Detector	Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 31, 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: 2.09→109.55 Å / Num. obs: 76651 / % possible obs: 96 % / Redundancy: 3.3 % / Net I/σ(I): 8.2
Reflection shell	Resolution: 2.09→2.13 Å

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Processing

Software

Name	Version	Classification
PHENIX	1.9_1692	refinement
XDS		data reduction
XDS		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 2A8A

2a8a

Resolution: 2.09→54.051 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 21

	R_factor	Num. reflection	% reflection
R_free	0.1912	3819	4.99 %
R_work	0.1761	-	-
obs	0.1769	76565	95.88 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Refinement step

Cycle: LAST / Resolution: 2.09→54.051 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6887	0	19	584	7490

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.013	7115
X-RAY DIFFRACTION	f_angle_d	1.237	9672
X-RAY DIFFRACTION	f_dihedral_angle_d	12.099	2626
X-RAY DIFFRACTION	f_chiral_restr	0.062	1058
X-RAY DIFFRACTION	f_plane_restr	0.007	1246

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 (%)
2.09-2.1165	0.2497	142	0.2495	2710	X-RAY DIFFRACTION	97
2.1165-2.1443	0.3011	142	0.2474	2604	X-RAY DIFFRACTION	96
2.1443-2.1737	0.2489	124	0.2454	2700	X-RAY DIFFRACTION	95
2.1737-2.2047	0.2693	146	0.2448	2582	X-RAY DIFFRACTION	94
2.2047-2.2377	0.2605	142	0.2476	2615	X-RAY DIFFRACTION	94
2.2377-2.2726	0.2782	127	0.2541	2617	X-RAY DIFFRACTION	94
2.2726-2.3099	0.2681	147	0.2483	2571	X-RAY DIFFRACTION	93
2.3099-2.3497	0.265	129	0.2446	2580	X-RAY DIFFRACTION	92
2.3497-2.3924	0.2617	149	0.2293	2606	X-RAY DIFFRACTION	93
2.3924-2.4385	0.27	117	0.2205	2587	X-RAY DIFFRACTION	94
2.4385-2.4882	0.2092	133	0.2105	2688	X-RAY DIFFRACTION	95
2.4882-2.5423	0.2351	137	0.2001	2701	X-RAY DIFFRACTION	95
2.5423-2.6015	0.2311	153	0.1926	2615	X-RAY DIFFRACTION	96
2.6015-2.6665	0.2304	114	0.1964	2719	X-RAY DIFFRACTION	96
2.6665-2.7386	0.2423	133	0.2003	2715	X-RAY DIFFRACTION	96
2.7386-2.8192	0.2475	154	0.1941	2719	X-RAY DIFFRACTION	97
2.8192-2.9102	0.1964	156	0.1932	2717	X-RAY DIFFRACTION	98
2.9102-3.0142	0.211	145	0.1846	2702	X-RAY DIFFRACTION	97
3.0142-3.1349	0.2005	141	0.1848	2754	X-RAY DIFFRACTION	98
3.1349-3.2775	0.2094	137	0.1912	2754	X-RAY DIFFRACTION	98
3.2775-3.4503	0.1984	151	0.1766	2756	X-RAY DIFFRACTION	98
3.4503-3.6664	0.1712	147	0.1721	2787	X-RAY DIFFRACTION	98
3.6664-3.9494	0.1482	166	0.1545	2756	X-RAY DIFFRACTION	99
3.9494-4.3467	0.1261	142	0.1292	2804	X-RAY DIFFRACTION	98
4.3467-4.9753	0.1411	134	0.1159	2762	X-RAY DIFFRACTION	96
4.9753-6.2669	0.1341	151	0.1403	2798	X-RAY DIFFRACTION	97
6.2669-54.0691	0.1544	160	0.1368	2827	X-RAY DIFFRACTION	94

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	0.0087	-0.0145	0.0089	0.0047	-0.0048	0.0093	-0.016	0.0813	-0.0097	-0.0525	-0.0727	0.0218	-0.0344	-0.0605	-0.0001	0.1877	0.0198	-0.0008	0.1591	-0.0376	0.1682	-15.6534	-49.1631	-40.6711
2	0.0037	-0.0001	0.0007	0.0012	-0.0004	0.0003	-0.0398	-0.0321	-0.0385	0.0092	-0.0038	0.0183	0.0318	-0.0384	-0	0.2559	-0.0532	0.1086	0.195	-0.0408	0.2845	-24.5989	-66.8626	-27.094
3	0.0471	-0.0241	0.0453	0.0188	0.0018	0.0692	-0.0146	-0.0117	-0.0086	-0.0122	-0.0873	0.034	-0.007	0.0017	-0.0193	0.1362	0.0219	0.0275	0.1477	-0.0153	0.1615	-14.1386	-49.471	-29.1507
4	0.0061	-0.0294	-0.0104	0.0583	-0.0158	0.0173	0.0375	0.0375	-0.0539	0.0399	-0.0396	0.0508	0.1241	0.0203	-0.0009	0.1462	0.029	0.0134	0.1527	-0.0022	0.1296	-7.3042	-58.6696	-37.1321
5	0.0023	-0.0056	0.0009	-0.0051	-0.0045	0.0026	0.0296	-0.0414	0.0186	0.0824	0.0073	0.0313	0.0294	0.0099	0.0028	0.167	0.0472	0.0599	0.1622	0.002	0.122	-12.8206	-49.8825	-11.7461
6	0.0073	-0.0057	0.005	0.0085	-0.008	0.0055	-0.0651	-0.0455	0.0365	0.0378	0.0325	-0.0486	-0.0157	-0.0407	-0	0.2412	0.0686	-0.0094	0.1953	-0.0026	0.1562	-2.171	-60.7077	-12.1366
7	0.0455	0.0699	0.0351	0.0876	0.0454	0.0365	-0.0602	0.0094	0.0547	-0.0013	0.0721	-0.0214	-0.0159	0.091	0.0058	0.1181	0.0422	-0.0047	0.2079	-0.0038	0.2027	10.9153	-53.9361	-34.9623
8	0.0211	-0.014	0.0151	0.1355	0.0085	0.0731	-0.1327	0.0021	0.0214	0.1645	0.0641	0.0276	-0.045	0.0812	-0.016	0.1499	0.0263	-0.0015	0.1769	-0.0105	0.1405	-6.0074	-45.8542	-18.1777
9	0.0051	0.0028	-0.0075	-0.0006	-0.0035	0.0003	-0.0206	-0.045	-0.0399	0.0602	-0.0163	0.0232	0.0526	-0.0435	0.0003	0.2899	-0.0183	0.2093	0.2866	0.0295	0.2888	-31.371	-51.2705	-7.2252
10	0.0308	-0.0436	-0.085	0.2367	0.0346	0.1834	0.0185	0.0646	-0.0139	0.037	-0.0567	0.0092	-0.0338	-0.0087	-0.0568	0.1362	0.0335	0.0177	0.1569	-0.0232	0.1726	-29.4395	-13.6132	-13.6843
11	0.1762	-0.1018	-0.0356	0.0673	-0.0165	0.1793	0.3477	0.0117	-0.0241	-0.5524	-0.1212	-0.0494	-0.2754	0.1145	0.1516	0.2944	0.1372	0.0063	0.1225	-0.0162	0.1219	-29.1949	-5.8802	-32.3239
12	0.1047	-0.1529	-0.1595	0.1249	0.2219	0.147	0.3913	0.0211	-0.2584	-0.9575	-0.2435	0.3168	0.0732	0.0788	0.0204	-0.0895	0.1818	0.2247	0.095	-0.1489	-0.0047	-24.6947	-16.232	-30.2999

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 1 through 46 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 47 through 68 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 69 through 123 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 124 through 201 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 202 through 235 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 236 through 277 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 278 through 321 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 322 through 403 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 404 through 429 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 1 through 181 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 182 through 301 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 302 through 429 )

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