PDB-7n18: Clostridium botulinum Neurotoxin Serotype A Light Chain Inhibited...

ID or keywords:

Entry

Database: PDB / ID: 7n18

Title

Clostridium botulinum Neurotoxin Serotype A Light Chain Inhibited by a Chiral Hydroxamic Acid

Components

Botulinum neurotoxin type A

Keywords

HYDROLASE/INHIBITOR / Botulinum protease / BoNT/A /

inhibitor /

HYDROLASE / HYDROLASE-INHIBITOR complex

Function / homology

Function and homology information

bontoxilysin / host cell presynaptic membrane / host cell cytoplasmic vesicle / host cell cytosol / protein transmembrane transporter activity /

metalloendopeptidase activity /

toxin activity / host cell plasma membrane /

proteolysis / zinc ion binding ...
Similarity search - Function

Biological species

Clostridium botulinum (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.03 Å

Authors

Silvaggi, N.R. / Allen, K.N.

Citation

Journal: Acs Med.Chem.Lett. / Year: 2021
Title: Use of Crystallography and Molecular Modeling for the Inhibition of the Botulinum Neurotoxin A Protease.
Authors: Turner, L.D. / Nielsen, A.L. / Lin, L. / Campedelli, A.J. / Silvaggi, N.R. / Chen, J.S. / Wakefield, A.E. / Allen, K.N. / Janda, K.D.

History

Deposition	May 27, 2021	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jul 6, 2022	Provider: repository / Type: Initial release
Revision 1.1	Oct 18, 2023	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2	Jan 17, 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 / _citation_author.identifier_ORCID / _citation_author.name

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	7n18.cif.gz	575.3 KB	Display	PDBx/mmCIF format
PDB format	pdb7n18.ent.gz	395.9 KB	Display	PDB format
PDBx/mmJSON format	7n18.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/n1/7n18 ftp://data.pdbj.org/pub/pdb/validation_reports/n1/7n18	HTTPS FTP

-
Related structure data

Related structure data	2imcS S: Starting model for refinement
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Botulinum neurotoxin type A

B: Botulinum neurotoxin type A

hetero molecules

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

1

A: Botulinum neurotoxin type A

hetero molecules

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

2

B: Botulinum neurotoxin type A

hetero molecules

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

Unit cell

Length a, b, c (Å)	72.990, 67.292, 97.487
Angle α, β, γ (deg.)	90.000, 105.149, 90.000
Int Tables number	4
Space group name H-M	P12₁1
Space group name Hall	P2yb
Symmetry operation	#1: x,y,z #2: -x,y+1/2,-z

#1: Protein	Botulinum neurotoxin type A / BoNT/A / Bontoxilysin-A / BOTOX Mass: 50965.430 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Clostridium botulinum (bacteria) / Gene: botA, bna, CBO0806, CLC_0862 / Plasmid: pET-15b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0DPI1
#2: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical	ChemComp-C7I / (3R)-3-(4-chlorophenyl)-N,5-dihydroxypentanamide Mass: 243.687 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₁H₁₄ClNO₃ / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical	ChemComp-C8I / (3S)-3-(4-chlorophenyl)-N,5-dihydroxypentanamide Mass: 243.687 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₁H₁₄ClNO₃ / Feature type: SUBJECT OF INVESTIGATION
#5: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 364 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.26 Å³/Da / Density % sol: 45.6 % Description: Thin rods. Microseeding improved morphology from needles.
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 10-15% polyethylene glycol [PEG] 2,000 monomethyl ester, 0.2-0.3 M K2HPO4, 0.1 M D,L-malic acid pH 7.0

-
Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: NSLS / Beamline: X12B / Wavelength: 1 Å
Detector	Type: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 2, 2008
Radiation	Monochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.02→50 Å / Num. obs: 95351 / % possible obs: 96.7 % / Redundancy: 3.6 % / B_iso Wilson estimate: 22 Å² / CC_1/2: 0.988 / CC star: 0.997 / R_merge(I) obs: 0.109 / R_pim(I) all: 0.068 / R_rim(I) all: 0.129 / Net I/σ(I): 10.8
Reflection shell	Resolution: 2.03→2.097 Å / Redundancy: 3.6 % / R_merge(I) obs: 0.511 / Mean I/σ(I) obs: 4.41 / Num. unique obs: 4629 / CC_1/2: 0.663 / CC star: 0.893 / R_pim(I) all: 0.315 / R_rim(I) all: 0.601 / % possible all: 78.3

-
Processing

Software

Name	Version	Classification
PHENIX	1.19.2_4158	refinement
HKL-2000		data reduction
HKL-2000		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 2IMC

2imc

Resolution: 2.03→31.91 Å / SU ML: 0.184 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.3324
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.1962	3307	3.47 %
R_work	0.1578	92044	-
obs	0.1591	95351	81.77 %

Solvent computation

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

Displacement parameters

B_iso mean: 31.88 Å²

Refinement step

Cycle: LAST / Resolution: 2.03→31.91 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6396	0	18	364	6778

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0107	6582
X-RAY DIFFRACTION	f_angle_d	1.0543	8888
X-RAY DIFFRACTION	f_chiral_restr	0.0594	968
X-RAY DIFFRACTION	f_plane_restr	0.0105	1141
X-RAY DIFFRACTION	f_dihedral_angle_d	15.4107	2425

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 (%)
2.03-2.05	0.2515	65	0.1927	1830	X-RAY DIFFRACTION	39.28
2.05-2.08	0.2229	81	0.1848	2220	X-RAY DIFFRACTION	47.04
2.08-2.12	0.2336	88	0.1804	2364	X-RAY DIFFRACTION	50.55
2.12-2.15	0.2353	93	0.1708	2592	X-RAY DIFFRACTION	54.99
2.15-2.19	0.1676	106	0.1706	2762	X-RAY DIFFRACTION	59.7
2.19-2.23	0.2029	105	0.1706	3003	X-RAY DIFFRACTION	64.03
2.23-2.27	0.2028	110	0.157	3209	X-RAY DIFFRACTION	67.97
2.27-2.32	0.2188	117	0.1615	3413	X-RAY DIFFRACTION	72.26
2.32-2.37	0.2316	134	0.1626	3556	X-RAY DIFFRACTION	76.24
2.37-2.42	0.236	137	0.1591	3784	X-RAY DIFFRACTION	80.51
2.42-2.48	0.2783	140	0.1621	3920	X-RAY DIFFRACTION	83.32
2.48-2.55	0.183	140	0.157	4153	X-RAY DIFFRACTION	88.48
2.55-2.63	0.2115	158	0.1624	4305	X-RAY DIFFRACTION	92.06
2.63-2.71	0.1941	165	0.1564	4487	X-RAY DIFFRACTION	95.84
2.71-2.81	0.1977	166	0.164	4564	X-RAY DIFFRACTION	97.85
2.81-2.92	0.1918	170	0.1636	4704	X-RAY DIFFRACTION	98.98
2.92-3.05	0.1995	166	0.1563	4664	X-RAY DIFFRACTION	99.61
3.05-3.21	0.1793	162	0.1537	4662	X-RAY DIFFRACTION	99.57
3.21-3.41	0.2143	166	0.1511	4646	X-RAY DIFFRACTION	99.44
3.41-3.68	0.1759	170	0.1535	4660	X-RAY DIFFRACTION	99.32
3.68-4.05	0.1665	169	0.1392	4646	X-RAY DIFFRACTION	99.32
4.05-4.63	0.18	165	0.1353	4648	X-RAY DIFFRACTION	99.38
4.63-5.83	0.1665	167	0.1518	4659	X-RAY DIFFRACTION	99.24
5.83-31.91	0.228	167	0.192	4593	X-RAY DIFFRACTION	97.64

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	2.91760621766	0.516746503821	0.692415616035	4.23352453806	-0.237111410004	3.39091940415	0.131393279034	-0.337922033727	-0.338434209997	0.533942085737	-0.0799546460801	-0.00560098807392	0.263626278371	0.108842297503	0.0174087264524	0.236705512267	0.0454998618594	-0.0442772766223	0.159114853386	0.0131527997746	0.189964360078	14.802	-3.429	32.079
2	1.67489002496	-0.684850143347	0.168831303365	2.58253379329	-0.541230270495	1.32265583673	-0.0397153413446	-0.228564182352	-0.147151557018	0.489948816711	0.0463746860304	0.13536291348	0.0216404315772	-0.0375786531455	0.0181591578403	0.196050572775	-0.00950439731483	0.0177140952361	0.161711741109	0.00334611594707	0.123947329731	8.189	0.174	31.618
3	1.62831267383	-0.675763925011	0.202797271945	2.43736150353	-0.219405080029	2.10458254979	0.0101834531126	-0.07040173519	-0.331547287915	0.228730068516	-0.075118235144	0.938372951151	0.0847184530499	-0.479247418837	0.0426733148709	0.142460259411	-0.0362195123483	0.0282032331015	0.248251313626	-0.0180793022677	0.393392932353	-6.158	3.252	23.838
4	2.17602765263	-0.561337580766	0.462141034223	2.80632837802	0.0663628194308	2.21488474769	0.110910829386	0.112274525132	-0.12361341277	-0.0731797451998	-0.141132966469	0.223934730276	-0.0940530464849	-0.10153397568	0.0208280040257	0.0933879383935	-0.0317414296	0.000193453133331	0.137810790693	0.0237496284941	0.145677474594	4.098	4.126	18.619
5	1.59940764843	0.120311448758	-0.365766135215	3.15743981774	-0.506250922185	2.07287163852	0.120769922679	-0.257788496091	0.156958121147	0.653975780378	-0.0377594702617	0.10962455316	-0.25536326412	0.0776322041321	-0.0125244189189	0.253611216309	-0.0108835773475	0.0476387860868	0.191930415552	-0.0289877864907	0.14464656847	18.156	27.084	29.768
6	1.68599775177	-0.563763161002	0.0631534780478	3.24261556942	0.493510832387	2.65784178458	0.0479285790792	-0.04915151107	0.332896830659	0.21138288672	-0.0747307523062	-0.493013374666	-0.442276477851	0.355915215032	-0.001394417986	0.213218514626	-0.0441148981091	-0.0211883412174	0.17324375019	0.0106109904137	0.217332121374	24.37	36.24	22.425
7	2.41214839706	-0.0639262233506	0.195390776247	3.11310651073	-0.488934293139	1.65145568303	0.0950400649187	-0.113918418496	0.0641946283762	0.322887608972	-0.13326003621	-0.375549448397	-0.102445191485	0.236685375792	0.0273297918484	0.110458019583	-0.0225842927362	-0.00490939157267	0.185260818233	-0.0084115797602	0.161166462277	30.658	23.217	22.782
8	4.03336126659	1.10771286773	-0.240489164356	4.02973064777	-1.300909515	3.61156484874	0.148560008757	0.809572217472	0.11395177167	-0.553986799172	-0.281752165835	-0.88331004582	-0.147980676227	0.991405302152	0.0386766038318	0.258412222065	0.0401420215306	0.143807121185	0.513829984836	0.0276078860248	0.434524052036	41.02	20.911	9.601
9	4.71553320176	0.110619575596	-0.227397922914	4.65798069972	0.210056681747	3.1054046551	-0.0443578464468	-0.283930776391	-0.442304295883	0.454442793816	-0.0871296264152	-0.501911509161	0.380383973629	0.42891775758	0.0541987713692	0.207668858268	0.063235010315	-0.0859361666105	0.300905351815	0.0713789940435	0.348187337615	38.25	3.741	27.338
10	3.21717385947	-1.82796312481	0.456980896398	3.29312641833	-0.801781088383	1.06070778158	0.223109180323	0.336620176296	0.0151690749836	-0.455666738875	-0.215483041919	-0.287563817971	0.0835142153599	0.18806894203	-0.00400648772211	0.186535672167	0.0251229502798	0.0165762181596	0.207323281609	-0.014534614117	0.140796241359	25.431	22.602	8.327
11	2.5461751455	1.26635427274	1.08200315458	6.3529467239	0.857227389262	5.85871902838	-0.116440311976	0.0517107182951	0.340266473307	-0.613206877906	0.104720569675	0.327173219298	-0.19377686725	-0.0553498222765	-0.00168106348338	0.214140481567	0.0348070767983	-0.0158427509153	0.206634000839	0.0685042447832	0.184775908765	14.959	35.52	1.499

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	( CHAIN A AND RESID -9:61 )	A	-9 - 61
2	X-RAY DIFFRACTION	2	( CHAIN A AND RESID 62:163 )	A	62 - 163
3	X-RAY DIFFRACTION	3	( CHAIN A AND RESID 164:298 )	A	164 - 298
4	X-RAY DIFFRACTION	4	( CHAIN A AND RESID 299:417 )	A	299 - 417
5	X-RAY DIFFRACTION	5	( CHAIN B AND RESID -9:48 )	B	-9 - 48
6	X-RAY DIFFRACTION	6	( CHAIN B AND RESID 49:99 )	B	49 - 99
7	X-RAY DIFFRACTION	7	( CHAIN B AND RESID 100:232 )	B	100 - 232
8	X-RAY DIFFRACTION	8	( CHAIN B AND RESID 233:274 )	B	233 - 274
9	X-RAY DIFFRACTION	9	( CHAIN B AND RESID 278:334 )	B	278 - 334
10	X-RAY DIFFRACTION	10	( CHAIN B AND RESID 335:390 )	B	335 - 390
11	X-RAY DIFFRACTION	11	( CHAIN B AND RESID 391:417 )	B	391 - 417

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi