PDB-6cwg: Ricin catalytic subunit bound go A9 VHH antibody

ID or keywords:

Entry

Database: PDB / ID: 6cwg

Title

Ricin catalytic subunit bound go A9 VHH antibody

Components

Ricin
VHH antibody

Keywords

IMMUNE SYSTEM / Ricin catalytic subunit / VHH antibody

Function / homology

Function and homology information

rRNA N-glycosylase / rRNA N-glycosylase activity / AMP binding / defense response / toxin activity / carbohydrate binding / killing of cells of another organism / negative regulation of translation
Similarity search - Function

Biological species

Ricinus communis (castor bean)

Vicugna pacos (alpaca)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 2.6 Å

Authors

Rudolph, M.J. / Mantis, N.

Funding support

United States, 1items

Citation

Journal: Protein Eng. Des. Sel. / Year: 2018
Title: Contribution of an unusual CDR2 element of a single domain antibody in ricin toxin binding affinity and neutralizing activity.
Authors: Rudolph, M.J. / Vance, D.J. / Kelow, S. / Angalakurthi, S.K. / Nguyen, S. / Davis, S.A. / Rong, Y. / Middaugh, C.R. / Weis, D.D. / Dunbrack Jr., R. / Karanicolas, J. / Mantis, N.J.

History

Deposition	Mar 30, 2018	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jan 16, 2019	Provider: repository / Type: Initial release
Revision 1.1	Dec 18, 2019	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2	Nov 6, 2024	Group: Data collection / Database references / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6cwg.cif.gz	316.8 KB	Display	PDBx/mmCIF format
PDB format	pdb6cwg.ent.gz	262.9 KB	Display	PDB format
PDBx/mmJSON format	6cwg.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	6cwg_validation.pdf.gz	450.1 KB	Display	wwPDB validaton report
Full document	6cwg_full_validation.pdf.gz	458.6 KB	Display
Data in XML	6cwg_validation.xml.gz	28.7 KB	Display
Data in CIF	6cwg_validation.cif.gz	39.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/cw/6cwg ftp://data.pdbj.org/pub/pdb/validation_reports/cw/6cwg	HTTPS FTP

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Related structure data

Related structure data	6cwkC C: citing same article (ref.)
Similar structure data	3egh-2 5hzy-d 5ms7-d 4lhq-1 5ms8-d 6n0w-d 1bu8-d 3egg-1 6akx-2 5y3e-d 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
Related items in Molecule of the Month	#161 - May 2013 Ricin similarity (15) #69 - Sep 2005 Cholera Toxin similarity (15) #21 - Sep 2001 Antibodies similarity (1) #256 - Apr 2021 SARS-CoV-2 Spike and Antibodies similarity (1)

Deposited unit

A: Ricin

B: VHH antibody

C: Ricin

D: VHH antibody

hetero molecules

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

1

A: Ricin

B: VHH antibody

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

2

C: Ricin

D: VHH antibody

hetero molecules

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

Unit cell

Length a, b, c (Å)	76.654, 76.654, 134.331
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	144
Space group name H-M	P3₁

#1: Protein	Ricin Mass: 30067.953 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Ricinus communis (castor bean) / Production host: Escherichia coli (E. coli) / References: UniProt: P02879, rRNA N-glycosylase
#2: Antibody	VHH antibody Mass: 14716.448 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vicugna pacos (alpaca) / Production host: Escherichia coli (E. coli)
#3: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 85 / 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: 2.54 Å³/Da / Density % sol: 51.65 %
Crystal grow	Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 10.5 Details: 200 mM Lithiuim sulfate, 100 mM CAPS pH 10.5, 2 M Ammonium sulfate

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 24-ID-E / Wavelength: 0.979 Å

Detector

Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 23, 2016

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.979 Å / Relative weight: 1

Reflection twin

Operator: h,-h-k,-l / Fraction: 0.5

Reflection

Resolution: 2.6→50 Å / Num. obs: 26739 / % possible obs: 100 % / Redundancy: 5.6 % / R_merge(I) obs: 0.091 / R_pim(I) all: 0.042 / R_rim(I) all: 0.1 / Χ²: 1.577 / Net I/σ(I): 9.1 / Num. measured all: 150691

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique obs	CC_1/2	R_pim(I) all	R_rim(I) all	Χ²	% possible all
2.6-2.64	5	0.607	1318	0.949	0.3	0.678	0.774	99.7
2.64-2.69	5.4	0.693	1359	0.955	0.328	0.767	0.828	100
2.69-2.74	5.6	0.533	1328	0.979	0.247	0.588	0.822	100
2.74-2.8	5.7	0.45	1362	0.985	0.207	0.495	0.853	100
2.8-2.86	5.7	0.488	1321	0.972	0.224	0.537	0.865	100
2.86-2.93	5.8	0.414	1340	0.98	0.19	0.456	0.921	100
2.93-3	5.8	0.305	1305	0.989	0.139	0.335	0.996	100
3-3.08	5.7	0.252	1357	0.99	0.116	0.277	1.07	100
3.08-3.17	5.8	0.208	1347	0.994	0.095	0.228	1.069	100
3.17-3.28	5.7	0.171	1310	0.994	0.078	0.188	1.24	100
3.28-3.39	5.8	0.137	1354	0.996	0.063	0.151	1.394	100
3.39-3.53	5.7	0.112	1308	0.996	0.052	0.124	1.59	100
3.53-3.69	5.7	0.105	1362	0.997	0.048	0.116	1.739	100
3.69-3.88	5.7	0.092	1321	0.996	0.043	0.101	2.049	99.9
3.88-4.13	5.6	0.081	1341	0.995	0.038	0.089	2.494	100
4.13-4.45	5.5	0.073	1340	0.996	0.035	0.081	3.022	100
4.45-4.89	5.5	0.065	1329	0.996	0.031	0.072	2.912	100
4.89-5.6	5.6	0.058	1343	0.998	0.027	0.064	2.347	100
5.6-7.05	5.7	0.05	1348	0.998	0.023	0.056	2.128	100
7.05-50	5.7	0.04	1346	0.998	0.018	0.044	2.453	99.9

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Phasing

Phasing	Method: molecular replacement

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Processing

Software

Name	Version	Classification
PHENIX	(1.11.1_2575: ???)	refinement
HKL-2000		data reduction
HKL-2000		data scaling
PHASER		phasing
PDB_EXTRACT	3.24	data extraction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.6→47.215 Å / Cross valid method: THROUGHOUT / σ(F): 2.63 / Phase error: 40.23 / Stereochemistry target values: TWIN_LSQ_F

	R_factor	Num. reflection	% reflection
R_free	0.2618	1269	4.67 %
R_work	0.2234	-	-
obs	0.2259	27158	99.95 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.6→47.215 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6018	0	2	85	6105

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.003	6147
X-RAY DIFFRACTION	f_angle_d	0.71	8342
X-RAY DIFFRACTION	f_dihedral_angle_d	10.558	3659
X-RAY DIFFRACTION	f_chiral_restr	0.043	917
X-RAY DIFFRACTION	f_plane_restr	0.005	1093

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 (%)
2.6013-2.7054	0.3989	142	0.3288	2878	X-RAY DIFFRACTION	95
2.7054-2.8283	0.3669	132	0.2975	2920	X-RAY DIFFRACTION	96
2.8283-2.9772	0.409	142	0.2937	2820	X-RAY DIFFRACTION	95
2.9772-3.1634	0.3282	128	0.2888	2894	X-RAY DIFFRACTION	96
3.1634-3.4071	0.3061	174	0.2595	2811	X-RAY DIFFRACTION	94
3.4071-3.749	0.3005	162	0.2442	2849	X-RAY DIFFRACTION	95
3.749-4.2892	0.3076	105	0.1991	2930	X-RAY DIFFRACTION	97
4.2892-5.3953	0.1665	132	0.1792	2860	X-RAY DIFFRACTION	96
5.3953-25.2595	0.213	152	0.1891	2862	X-RAY DIFFRACTION	95

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	2.8402	1.4637	0.503	6.1147	0.3568	1.706	-0.3508	0.0919	-0.6611	0.4462	-0.0351	-0.2423	1.5632	0.555	0.3849	1.6033	0.339	0.1615	0.9943	-0.0298	0.4281	63.2545	48.8676	-46.8893
2	3.0166	1.004	-0.5354	1.1408	0.2053	2.8979	-0.0646	0.3347	-0.5468	-0.0089	-0.1309	-0.2466	0.7128	0.2921	0.1667	1.2822	0.167	0.0088	1.0827	-0.0612	0.2318	64.9573	59.2997	-49.61
3	4.5331	1.1026	1.6932	0.7564	-1.3996	7.3599	-0.1359	0.3726	-0.3013	-0.0687	-0.0276	-0.1322	0.775	0.0484	0.1453	1.0165	0.1694	0.0538	0.9818	-0.1127	0.2688	57.243	61.463	-58.7459
4	2.0306	0.1377	-0.3378	0.4645	-0.091	3.7324	-0.1683	0.3218	-0.2543	-0.1076	0.0246	0.058	0.7634	-0.2826	0.1313	1.4107	-0.065	0.1029	1.1022	-0.153	0.17	50.6839	57.4872	-56.3119
5	5.7306	-1.0216	0.5089	6.9616	2.0397	2.0036	-0.4111	-0.4388	-0.8514	-0.3894	-0.0342	0.1541	2.4723	-0.8524	0.4264	1.718	-0.009	0.1363	1.0175	-0.0387	0.4206	50.2744	49.0353	-37.9353
6	0.9145	0.5767	0.637	1.5655	0.9732	3.7748	0.129	-0.184	0.0839	0.1854	-0.1123	-0.0137	-0.0427	0.095	-0.0245	1.0687	0.1927	0.0063	0.9802	-0.0318	0.235	56.971	68.5083	-32.5937
7	2.2596	-1.6274	0.2385	3.0601	-0.8122	5.4169	-0.0613	0.128	0.0877	-0.0397	0.0746	0.0897	-1.0947	-0.472	-0.0211	1.1537	-0.0185	-0.0449	1.1374	-0.0373	0.3207	40.6447	81.4094	-84.0423
8	2.0983	-0.3068	1.2528	2.2083	0.0269	2.8622	-0.0732	-0.0351	0.0556	0.3004	0.0917	-0.0365	0.1616	0.1159	-0.0057	1.0517	-0.1309	0.0036	1.3412	0.0223	0.0543	47.2079	70.9396	-77.0102
9	3.8162	-0.8867	1.1554	7.2472	2.3087	8.9777	-0.0788	0.457	0.0375	-0.4345	0.1188	-0.5754	-0.4964	0.9833	-0.0364	0.977	-0.1754	0.03	1.1901	0.0095	0.3828	50.4474	77.6677	-79.8988
10	5.5812	-5.7543	-5.5567	6.0691	6.7081	2.0001	-0.7188	0.4424	0.349	-0.8547	-0.4709	0.5447	-1.1691	0.3759	1.1926	1.0456	-0.0893	-0.1169	1.183	-0.1359	0.3965	47.2084	81.1411	-82.108
11	3.1829	1.3055	1.9452	4.8496	1.7662	1.4062	-0.1001	0.6224	-0.0475	0.1011	-0.532	-0.2436	-0.2282	0.3625	0.6239	1.3049	-0.1633	-0.2374	1.4557	-0.075	0.4464	46.9516	76.5774	-95.3673
12	2.7142	-3.7859	5.2225	5.2794	-7.2846	2.0001	-0.1093	0.0933	0.1436	-0.0383	0.0459	-0.0884	-0.6895	0.0866	0.059	1.0085	-0.014	0.092	1.0725	-0.0308	0.1806	40.8157	71.7511	-81.463
13	2.2029	-1.341	1.3015	2.7932	-1.7953	4.0559	-0.0542	0.0778	-0.0955	-0.1362	-0.0677	0.1266	0.0645	-0.1491	0.1029	1.0786	-0.1191	-0.0116	1.0903	-0.0103	0.1989	43.8263	68.4259	-78.7255
14	2.2705	0.7367	-1.3444	2.3146	0.0872	3.3453	-0.1724	0.1279	-0.2057	0.244	-0.0881	0.4825	0.0175	-1.3107	0.2337	0.9412	-0.0023	0.0938	1.5685	-0.0513	0.3059	15.5578	38.9956	-42.6711
15	1.0126	-0.9056	0.0566	2.4043	-0.1048	3.3963	-0.0099	-0.2587	0.0714	0.6377	-0.07	0.1908	-0.0257	-0.3061	0.0825	1.0547	0.0103	0.0963	1.2133	-0.0056	0.2222	25.1263	37.6224	-29.6523
16	0.8186	-0.5514	-0.4159	1.3905	-0.3264	5.6865	-0.0654	-0.2122	-0.2981	0.3935	-0.0351	0.3064	1.0015	-0.5635	0.1114	1.249	-0.2637	0.2078	1.2617	0.007	0.2928	23.8584	23.6477	-38.2725
17	0.8373	-0.1531	-0.3506	1.7073	-0.0383	4.1283	-0.1587	-0.0264	-0.1807	-0.1377	-0.0022	0.1039	0.5583	-0.3866	0.1533	0.9386	-0.0243	0.0592	1.2244	0.0039	0.1973	27.2543	31.4188	-57.1256
18	1.3646	0.3402	1.4207	0.2663	0.4783	3.9419	-0.0946	0.542	0.0609	-0.1964	0.2714	0.1253	-0.8359	-0.1876	-0.1791	0.8744	0.0715	0.0706	1.2953	0.0818	0.3447	27.147	45.9858	-55.0116
19	8.6832	3.4689	5.8942	3.1327	2.1103	5.2704	-0.3772	-0.2604	-0.333	-0.1323	0.0543	-0.1004	-0.4423	0.8847	0.3254	1.178	0.0564	0.0538	0.967	-0.0025	0.3689	50.6609	29.0528	-6.8761
20	2.8968	-3.4577	-3.9337	7.5871	8.3817	2.0002	-0.2948	0.171	-0.0613	-0.6899	-0.8252	0.3137	-1.6273	-0.9129	1.115	1.1315	-0.0537	0.0371	1.1844	-0.0356	0.3334	49.7767	34.958	-6.132
21	5.7164	-5.0953	8.3602	4.5422	-7.4526	2.0003	1.6276	1.3395	-0.5267	-2.0012	-0.1842	0.3144	0.0936	1.0688	-1.4423	1.249	0.1096	0.0041	1.1123	0.0673	0.4623	42.8934	30.8288	-26.8087
22	1.2554	0.0657	0.7338	0.317	0.2342	0.5504	-0.1565	-0.0806	-0.0262	0.4385	0.2998	-0.0028	-0.1949	-0.9481	-0.1379	1.1588	0.0257	-0.0448	0.9045	0.0645	0.2169	38.7713	29.6289	-9.9723
23	1.5647	-0.1299	0.4824	3.9051	-3.4342	3.9902	-0.016	-0.0282	0.051	-0.1596	0.0342	0.1352	0.245	-0.0876	-0.0359	1.2046	0.0554	0.0594	1.1231	-0.0494	0.0998	35.5628	33.5081	-10.3384
24	6.4983	0.9719	3.0157	4.4395	-0.2155	2.0007	-0.2723	-1.2447	0.609	0.6734	-0.0401	0.1452	-1.643	-0.1621	0.3054	1.4642	0.0636	-0.0515	1.0445	-0.0166	0.3874	39.8618	38.9826	-7.5627
25	5.0651	-0.4333	-1.6988	4.2574	-2.9264	4.4767	-0.0931	0.1257	0.3242	-0.0336	-0.0741	-0.0848	-1.0939	1.5259	0.1645	1.1405	-0.0485	0.1403	1.0318	0.0229	0.3356	47.8098	36.2086	-15.8263
26	2.0213	1.4552	2.5278	1.6144	0.3066	7.1784	-0.0332	-0.3796	0.2551	0.3139	-0.0991	0.0853	-0.8698	-0.265	0.136	1.2106	0.0145	0.064	1.126	-0.0228	0.2001	42.5295	31.3711	-2.9322
27	6.3407	-1.7756	0.7514	2.2838	0.3679	4.1278	0.0078	0.0563	-0.2816	0.191	-0.034	0.0654	0.604	-0.1728	0.0291	1.1859	-0.0425	0.0502	0.9819	0.0205	0.1296	34.0252	27.3732	-16.8716
28	4.8553	1.2534	0.7951	6.0169	7.8224	2	-0.1729	-0.4758	-0.159	1.5045	0.3898	-0.6029	-0.3328	0.0287	-0.2173	1.2376	-0.0517	-0.097	0.9677	0.1793	0.4544	48.8268	29.4467	2.9157

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resseq 5:32)
2	X-RAY DIFFRACTION	2	chain 'A' and (resseq 33:75)
3	X-RAY DIFFRACTION	3	chain 'A' and (resseq 76:97)
4	X-RAY DIFFRACTION	4	chain 'A' and (resseq 98:180)
5	X-RAY DIFFRACTION	5	chain 'A' and (resseq 181:201)
6	X-RAY DIFFRACTION	6	chain 'A' and (resseq 202:267)
7	X-RAY DIFFRACTION	7	chain 'B' and (resseq 3:24)
8	X-RAY DIFFRACTION	8	chain 'B' and (resseq 25:62)
9	X-RAY DIFFRACTION	9	chain 'B' and (resseq 63:79)
10	X-RAY DIFFRACTION	10	chain 'B' and (resseq 80:86)
11	X-RAY DIFFRACTION	11	chain 'B' and (resseq 87:93)
12	X-RAY DIFFRACTION	12	chain 'B' and (resseq 94:101)
13	X-RAY DIFFRACTION	13	chain 'B' and (resseq 102:129)
14	X-RAY DIFFRACTION	14	chain 'C' and (resseq 5:75)
15	X-RAY DIFFRACTION	15	chain 'C' and (resseq 76:122)
16	X-RAY DIFFRACTION	16	chain 'C' and (resseq 123:180)
17	X-RAY DIFFRACTION	17	chain 'C' and (resseq 181:247)
18	X-RAY DIFFRACTION	18	chain 'C' and (resseq 248:264)
19	X-RAY DIFFRACTION	19	chain 'D' and (resseq 3:13)
20	X-RAY DIFFRACTION	20	chain 'D' and (resseq 14:23)
21	X-RAY DIFFRACTION	21	chain 'D' and (resseq 24:32)
22	X-RAY DIFFRACTION	22	chain 'D' and (resseq 33:39)
23	X-RAY DIFFRACTION	23	chain 'D' and (resseq 40:62)
24	X-RAY DIFFRACTION	24	chain 'D' and (resseq 63:75)
25	X-RAY DIFFRACTION	25	chain 'D' and (resseq 76:85)
26	X-RAY DIFFRACTION	26	chain 'D' and (resseq 86:101)
27	X-RAY DIFFRACTION	27	chain 'D' and (resseq 102:122)
28	X-RAY DIFFRACTION	28	chain 'D' and (resseq 123:129)

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News

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