PDB-5vmr: Receptor binding domain of BoNT/B in complex with mini-protein bi...

ID or keywords:

Entry

Database: PDB / ID: 5vmr

Title

Receptor binding domain of BoNT/B in complex with mini-protein binder Bot.2110.4

Components

Bot.2110.4
Botulinum neurotoxin type B

Keywords

TOXIN / mini-protein binder / inhibitor

Function / homology

Function and homology information

Toxicity of botulinum toxin type B (botB) / bontoxilysin / host cell presynaptic membrane / host cell cytoplasmic vesicle / host cell cytosol / protein transmembrane transporter activity / metalloendopeptidase activity / toxin activity / lipid binding / host cell plasma membrane ...
Similarity search - Function

Biological species

Clostridium botulinum (bacteria)
unidentified (others)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.95 Å

Authors

Jin, R. / Lam, K. / Yao, G.

Citation

Journal: Nature / Year: 2017
Title: Massively parallel de novo protein design for targeted therapeutics.
Authors: Chevalier, A. / Silva, D.A. / Rocklin, G.J. / Hicks, D.R. / Vergara, R. / Murapa, P. / Bernard, S.M. / Zhang, L. / Lam, K.H. / Yao, G. / Bahl, C.D. / Miyashita, S.I. / Goreshnik, I. / ...

History

Deposition	Apr 28, 2017	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Sep 20, 2017	Provider: repository / Type: Initial release
Revision 1.1	Oct 18, 2017	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.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	Nov 29, 2017	Group: Data collection / Category: diffrn_source Item: _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.type
Revision 1.3	Oct 4, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4	Oct 23, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5vmr.cif.gz	411.3 KB	Display	PDBx/mmCIF format
PDB format	pdb5vmr.ent.gz	335.9 KB	Display	PDB format
PDBx/mmJSON format	5vmr.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	5vmr_validation.pdf.gz	459.5 KB	Display	wwPDB validaton report
Full document	5vmr_full_validation.pdf.gz	473.1 KB	Display
Data in XML	5vmr_validation.xml.gz	39.7 KB	Display
Data in CIF	5vmr_validation.cif.gz	57.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/vm/5vmr ftp://data.pdbj.org/pub/pdb/validation_reports/vm/5vmr	HTTPS FTP

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Related structure data

Related structure data	5vidSC 5vliC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	4bva-d 4xbo-d 1srp-d 7nc7-d 5d7w-d 1wcv-1 5ako-d 3nze-3 1go7-d 5uaw-2 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) 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: Botulinum neurotoxin type B

B: Botulinum neurotoxin type B

C: Bot.2110.4

D: Bot.2110.4

115 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Botulinum neurotoxin type B

C: Bot.2110.4

defined by author&software
Evidence: gel filtration
57.5 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Botulinum neurotoxin type B

D: Bot.2110.4

defined by author&software
Evidence: gel filtration
57.5 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	38.698, 246.477, 64.364
Angle α, β, γ (deg.)	90.00, 102.90, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Botulinum neurotoxin type B / BoNT/B / Bontoxilysin-B Mass: 52534.145 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Clostridium botulinum (bacteria) / Gene: botB / Production host: Escherichia coli (E. coli) / References: UniProt: P10844, bontoxilysin
#2: Protein/peptide	Bot.2110.4 Mass: 4928.769 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) unidentified (others)
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 575 / Source method: isolated from a natural source / Formula: H₂O
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: 2.6 Å³/Da / Density % sol: 52.76 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, hanging drop Details: 0.1 M Magnesium acetate, 0.1 M Sodium acetate pH 5.0, 10 % PEG8000

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97918 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 17, 2017
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97918 Å / Relative weight: 1
Reflection	Resolution: 1.95→19.97 Å / Num. obs: 84657 / % possible obs: 99.6 % / Redundancy: 3.5 % / R_merge(I) obs: 0.058 / Net I/σ(I): 7.7
Reflection shell	Resolution: 1.95→1.99 Å / Redundancy: 3.5 % / R_merge(I) obs: 0.372 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 4433 / CC_1/2: 0.836 / % possible all: 99.5

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Processing

Software

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

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5VID

5vid

Resolution: 1.95→19.969 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.89

	R_factor	Num. reflection	% reflection
R_free	0.2059	4205	5.01 %
R_work	0.1814	-	-
obs	0.1827	83967	98.89 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.95→19.969 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7691	0	0	575	8266

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	7915
X-RAY DIFFRACTION	f_angle_d	1.111	10662
X-RAY DIFFRACTION	f_dihedral_angle_d	13.191	2949
X-RAY DIFFRACTION	f_chiral_restr	0.05	1102
X-RAY DIFFRACTION	f_plane_restr	0.005	1358

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 (%)
1.95-1.9722	0.2574	151	0.2462	2537	X-RAY DIFFRACTION	97
1.9722-1.9953	0.3023	127	0.2401	2609	X-RAY DIFFRACTION	97
1.9953-2.0196	0.2664	142	0.2299	2645	X-RAY DIFFRACTION	97
2.0196-2.0452	0.2531	147	0.2348	2612	X-RAY DIFFRACTION	98
2.0452-2.0721	0.2714	124	0.2256	2604	X-RAY DIFFRACTION	98
2.0721-2.1004	0.2625	136	0.2166	2651	X-RAY DIFFRACTION	98
2.1004-2.1304	0.2375	129	0.211	2646	X-RAY DIFFRACTION	97
2.1304-2.1622	0.2381	135	0.2163	2693	X-RAY DIFFRACTION	99
2.1622-2.1959	0.2376	117	0.211	2561	X-RAY DIFFRACTION	99
2.1959-2.2319	0.2416	148	0.2045	2692	X-RAY DIFFRACTION	99
2.2319-2.2703	0.2199	126	0.2069	2698	X-RAY DIFFRACTION	99
2.2703-2.3115	0.2489	139	0.2065	2626	X-RAY DIFFRACTION	99
2.3115-2.3559	0.2238	115	0.192	2657	X-RAY DIFFRACTION	99
2.3559-2.4039	0.2228	134	0.2095	2764	X-RAY DIFFRACTION	99
2.4039-2.4561	0.2255	135	0.202	2604	X-RAY DIFFRACTION	99
2.4561-2.5131	0.2455	144	0.2009	2646	X-RAY DIFFRACTION	99
2.5131-2.5758	0.2302	153	0.1963	2767	X-RAY DIFFRACTION	99
2.5758-2.6453	0.2259	135	0.1994	2572	X-RAY DIFFRACTION	99
2.6453-2.723	0.2412	138	0.2054	2677	X-RAY DIFFRACTION	99
2.723-2.8107	0.1953	145	0.2044	2692	X-RAY DIFFRACTION	99
2.8107-2.9108	0.2293	161	0.2025	2644	X-RAY DIFFRACTION	100
2.9108-3.027	0.2299	139	0.1963	2670	X-RAY DIFFRACTION	100
3.027-3.1642	0.1991	149	0.1968	2662	X-RAY DIFFRACTION	99
3.1642-3.3303	0.2112	162	0.1871	2649	X-RAY DIFFRACTION	100
3.3303-3.5379	0.2027	144	0.1831	2729	X-RAY DIFFRACTION	100
3.5379-3.8093	0.2102	137	0.1729	2668	X-RAY DIFFRACTION	100
3.8093-4.1895	0.177	164	0.153	2673	X-RAY DIFFRACTION	100
4.1895-4.7884	0.1642	160	0.1332	2693	X-RAY DIFFRACTION	100
4.7884-6.0056	0.1668	144	0.1509	2673	X-RAY DIFFRACTION	100
6.0056-19.9696	0.1828	125	0.1586	2748	X-RAY DIFFRACTION	100

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	1.0713	0.2196	0.2426	1.7805	0.4303	1.5007	0.0571	-0.0395	0.0708	0.1052	0.0575	-0.0494	0.1526	0.0108	-0.1058	0.2286	-0.0011	-0.032	0.2635	-0.0053	0.2173	-5.2845	23.7117	99.7362
2	1.8811	0.3555	0.0978	2.0282	0.7788	1.8729	0.0558	-0.2556	0.2277	0.2155	0.0081	0.1037	0.1789	-0.0621	-0.0422	0.2508	-0.0297	-0.0121	0.3011	-0.0164	0.1916	-9.3152	23.9183	104.5331
3	0.7376	0.1584	0.3978	0.9565	1.1787	2.4492	0.0734	0.0766	0.0785	-0.0829	0.0352	-0.0704	0.0318	-0.0305	-0.0703	0.2465	-0.0119	-0.0454	0.2738	0.0372	0.2585	-11.3414	20.7069	83.1217
4	1.3045	-0.269	0.3005	1.2224	0.4535	2.8218	0.2318	0.2082	-0.2367	-0.1381	0.0087	-0.0545	0.8082	0.0244	-0.1689	0.4025	-0.0045	-0.1094	0.2948	-0.0117	0.2752	-10.1378	5.0075	72.5702
5	1.6277	0.097	1.3293	1.579	0.9478	3.344	0.1099	0.3983	-0.0726	-0.3471	-0.0178	0.087	0.1386	0.0364	-0.1006	0.3355	0.0002	-0.0555	0.3822	0.0166	0.2307	-17.6214	12.1085	61.1063
6	2.0141	-0.155	0.676	3.6591	1.7543	2.4098	0.0865	0.2544	-0.1485	-0.4765	0.0169	0.5639	0.3568	-0.3125	-0.1315	0.4554	-0.0692	-0.1256	0.489	0.0149	0.2948	-23.339	7.992	62.8472
7	1.3464	0.2953	0.5328	1.9302	0.6802	2.6577	0.1747	-0.0124	0.0925	-0.092	-0.0348	0.2412	0.2524	-0.4955	-0.1596	0.2541	-0.0411	-0.017	0.3927	0.0342	0.2269	-19.6035	14.2811	74.9849
8	0.8856	-0.0133	-0.1063	1.4516	-0.5981	1.4808	0.0744	-0.0733	0.0704	0.1574	0.0097	0.0875	-0.1282	-0.0234	-0.0888	0.2584	-0.0095	0.0636	0.2524	-0.0379	0.3544	-3.3675	67.9894	102.7086
9	2.1093	0.3804	-0.145	1.6221	-0.4391	1.5749	0.0021	-0.4161	0.0601	0.354	0.0131	-0.0543	-0.1343	0.1017	-0.0428	0.3599	-0.0149	0.0673	0.332	-0.046	0.3866	0.6784	67.1179	107.4621
10	0.8589	-0.1206	-0.3958	2.063	-0.8395	1.8605	0.1624	0.0455	0.1834	-0.1499	0.0108	-0.0307	-0.3058	0.016	-0.142	0.2984	-0.0142	0.0969	0.2625	-0.0378	0.4398	3.3259	80.9113	86.0655
11	1.1088	-0.0461	-0.6269	2.9625	-0.9619	2.2784	0.2515	0.2199	0.1702	-0.7634	-0.0777	0.1387	-0.145	0.1095	-0.1729	0.6301	0.0484	0.0987	0.4088	0.0065	0.4975	3.7571	84.3881	66.9914
12	1.4355	-0.326	-0.3076	2.4804	-1.2184	1.9109	0.3617	0.1913	0.1169	-0.7596	-0.2293	-0.3795	-0.2367	0.5095	-0.025	0.4995	-0.0002	0.1643	0.4005	-0.0161	0.5324	11.7682	83.2835	73.7192
13	3.6893	-0.0566	1.1159	2.9138	0.3848	4.8836	-0.0807	0.6332	0.2171	-0.3853	0.0018	0.0957	0.6693	0.0369	0.121	0.6758	0.0488	-0.1913	0.5133	-0.0627	0.4205	-18.0999	-3.4299	49.4146
14	2.9741	-3.0681	0.8831	3.4759	-1.0578	3.4931	0.0193	-2.1571	0.9247	1.8326	-0.0515	0.6194	-0.2997	0.2947	0.1129	0.8964	-0.1155	0.2183	0.8769	-0.43	0.6897	-18.2065	-12.3863	44.4287
15	4.3897	0.2217	-0.8816	2.572	-0.4489	4.6341	0.2564	1.0165	-0.145	-0.7172	0.0043	-0.194	-0.5551	0.1525	-0.0899	1.2051	0.0964	0.4506	0.6266	0.079	0.7715	8.6862	100.7753	55.7126
16	9.6256	1.2601	1.2714	4.807	-4.4743	4.8121	0.3178	-2.246	0.0982	1.9951	-0.49	-0.1201	1.2067	-0.9731	0.2529	0.9523	0.0377	0.2705	0.9399	0.1035	0.8685	8.4036	109.7874	51.2599

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 861 through 1012 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 1013 through 1053 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 1054 through 1112 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 1113 through 1181 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 1182 through 1221 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 1222 through 1260 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 1261 through 1291 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 861 through 1012 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 1013 through 1053 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 1054 through 1149 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 1150 through 1221 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 1222 through 1291 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 2 through 28 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 29 through 39 )
15	X-RAY DIFFRACTION	15	chain 'D' and (resid 2 through 28 )
16	X-RAY DIFFRACTION	16	chain 'D' and (resid 29 through 39 )

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