PDB-3q9o: Full-length Cholix toxin from Vibrio cholerae in complex with NAD

ID or keywords:

Entry

Database: PDB / ID: 3q9o

Title

Full-length Cholix toxin from Vibrio cholerae in complex with NAD

Components

exotoxin A

Keywords

TRANSFERASE / receptor binding domain / beta barrel / translocation / six alpha-helix bundle / alpha-beta complex / ADP-ribosylating factor / diphthamide on eukaryotic elongation factor 2

Function / homology

Function and homology information

NAD+-diphthamide ADP-ribosyltransferase / NAD+-diphthamide ADP-ribosyltransferase activity / nucleotidyltransferase activity / toxin activity
Similarity search - Function

Biological species

Vibrio cholerae (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.793 Å

Authors

Merrill, A.R. / Jorgensen, R. / Fieldhouse, R.J.

Citation

Journal: J.Biol.Chem. / Year: 2012
Title: The 1.8 a cholix toxin crystal structure in complex with NAD+ and evidence for a new kinetic model.
Authors: Fieldhouse, R.J. / Jorgensen, R. / Lugo, M.R. / Merrill, A.R.

History

Deposition	Jan 9, 2011	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jan 4, 2012	Provider: repository / Type: Initial release
Revision 1.1	May 9, 2012	Group: Database references
Revision 1.2	Jul 4, 2012	Group: Database references
Revision 1.3	Sep 13, 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_ref_seq_dif / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4	Oct 30, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3q9o.cif.gz	267.7 KB	Display	PDBx/mmCIF format
PDB format	pdb3q9o.ent.gz	215.8 KB	Display	PDB format
PDBx/mmJSON format	3q9o.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	3q9o_validation.pdf.gz	823.7 KB	Display	wwPDB validaton report
Full document	3q9o_full_validation.pdf.gz	828.8 KB	Display
Data in XML	3q9o_validation.xml.gz	27.1 KB	Display
Data in CIF	3q9o_validation.cif.gz	40.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/q9/3q9o ftp://data.pdbj.org/pub/pdb/validation_reports/q9/3q9o	HTTPS FTP

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Related structure data

Related structure data	2q5tS 2q6m 3ess S: Starting model for refinement
Similar structure data	6tbi-7 2xz9-d 6tbg-3 6tbg-5 6tbg-4 6tbh-1 6tbg-7 5zlf-1 6mri-1 6tbf-5 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	#69 - Sep 2005 Cholera Toxin similarity (1)

Deposited unit

A: exotoxin A

hetero molecules

72.8 kDa, 1 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)	50.929, 89.083, 80.283
Angle α, β, γ (deg.)	90.000, 95.110, 90.000
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	exotoxin A / cholix toxin Mass: 71872.984 Da / Num. of mol.: 1 / Fragment: UNP residues 33-666 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vibrio cholerae (bacteria) / Strain: TP / Gene: chxa, toxA / Plasmid: PET28A+ / Production host: Escherichia coli (E. coli) / Strain (production host): ER2566 / References: UniProt: Q5EK40
#2: Chemical	ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE Mass: 663.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂₁H₂₇N₇O₁₄P₂ / Comment: NAD*YM
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 402 / 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: 2.52 Å³/Da / Density % sol: 51.26 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 23% PEG10000, 7.5% ethylene glycol, 0.1 M HEPES, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

CLSI

/ Beamline: 08ID-1 / Wavelength: 0.97934

Detector

Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jan 23, 2008 / Details: Vertically focusing mirror (VFM)

Radiation

Monochromator: White beam slits, cryo-cooled first and sagittally bent second crystal of double crystal monochromator (DCM)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.97934 Å / Relative weight: 1

Reflection

Resolution: 1.793→20 Å / Num. all: 64910 / Num. obs: 64910 / % possible obs: 97.4 % / Observed criterion σ(I): -3 / Redundancy: 3.6 % / B_iso Wilson estimate: 25.9 Å² / R_merge(I) obs: 0.07 / Net I/σ(I): 12

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique all	Χ²	Diffraction-ID	% possible all
1.8-1.86	2.6	0.476	5409	0.949	1	81.6
1.86-1.94	3	0.375	6216	1.117	1	93.4
1.94-2.03	3.4	0.282	6574	1.174	1	99
2.03-2.13	3.7	0.222	6647	1.28	1	99.9
2.13-2.27	3.8	0.167	6600	1.319	1	100
2.27-2.44	3.8	0.131	6681	1.371	1	100
2.44-2.69	3.8	0.101	6663	1.31	1	100
2.69-3.07	3.8	0.082	6658	1.429	1	100
3.07-3.87	3.8	0.059	6697	1.129	1	100
3.87-20	3.7	0.04	6765	1.033	1	99.8

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Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
PHENIX	1.6_289	refinement
PDB_EXTRACT	3.1	data extraction
Macromolecular	Crystallography Data Collection (MXDC) GUI	data collection
HKL-2000		data reduction
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2Q5T

2q5t

Resolution: 1.793→19.931 Å / Occupancy max: 1 / Occupancy min: 0.24 / FOM work R set: 0.8611 / SU ML: 0.21 / Isotropic thermal model: ISOTROPIC WITH 20 TLS GROUPS / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.33 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2035	3291	5.07 %	RANDOM
R_work	0.163	-	-	-
obs	0.1651	64881	97.06 %	-
all	-	64881	-	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 60.135 Å² / k_sol: 0.4 e/Å³

Displacement parameters

B_iso max: 133.35 Å² / B_iso mean: 35.6257 Å² / B_iso min: 13.67 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.431 Å²	-0 Å²	-0.2449 Å²
2-	-	-0.2074 Å²	-0 Å²
3-	-	-	-0.2236 Å²

Refinement step

Cycle: LAST / Resolution: 1.793→19.931 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4745	0	62	402	5209

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.013	5046
X-RAY DIFFRACTION	f_angle_d	1.415	6900
X-RAY DIFFRACTION	f_chiral_restr	0.1	773
X-RAY DIFFRACTION	f_plane_restr	0.006	905
X-RAY DIFFRACTION	f_dihedral_angle_d	17.801	1882

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 24

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
1.7931-1.8187	0.3095	89	0.2647	1878	1967	69
1.8187-1.8459	0.319	128	0.2349	2152	2280	84
1.8459-1.8747	0.2481	115	0.2305	2369	2484	89
1.8747-1.9054	0.256	134	0.2198	2481	2615	93
1.9054-1.9382	0.2778	133	0.2155	2515	2648	96
1.9382-1.9734	0.2501	138	0.1893	2585	2723	99
1.9734-2.0114	0.2147	145	0.1773	2611	2756	100
2.0114-2.0524	0.2114	143	0.1703	2641	2784	100
2.0524-2.0969	0.2204	152	0.1607	2594	2746	100
2.0969-2.1457	0.1954	136	0.1591	2665	2801	100
2.1457-2.1993	0.1994	137	0.1584	2620	2757	100
2.1993-2.2586	0.2242	140	0.1606	2645	2785	100
2.2586-2.325	0.2141	119	0.1605	2675	2794	100
2.325-2.3999	0.1904	141	0.1571	2623	2764	100
2.3999-2.4856	0.2302	138	0.1536	2635	2773	100
2.4856-2.5849	0.1832	153	0.162	2644	2797	100
2.5849-2.7023	0.198	155	0.1621	2641	2796	100
2.7023-2.8443	0.2316	139	0.1609	2637	2776	100
2.8443-3.022	0.2086	132	0.1643	2674	2806	100
3.022-3.2544	0.2237	130	0.1612	2642	2772	100
3.2544-3.5802	0.1781	140	0.1486	2644	2784	100
3.5802-4.0943	0.1594	133	0.14	2682	2815	100
4.0943-5.1437	0.176	152	0.1326	2667	2819	100
5.1437-19.9324	0.1776	169	0.169	2670	2839	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	1.4068	-0.8518	0.0982	1.4177	0.2127	0.108	0.2204	0.8492	0.0718	-1.1227	-0.1913	0.1867	-0.7806	-0.1998	0.0004	0.6943	0.0919	0.0779	0.5509	-0.0315	0.206	33.2662	44.5611	32.2417
2	1.5742	0.2158	-0.3462	1.0474	-0.2695	3.0624	0.0861	0.2176	-0.0919	-0.4105	-0.0199	-0.1391	-0.2453	0.1529	-0.0509	0.332	0.0411	0.0535	0.3091	-0.014	0.2067	36.6689	42.3819	44.4102
3	1.0133	0.2073	-0.6432	0.6528	-0.4679	2.1119	0.1969	0.0517	-0.1104	-0.2862	-0.0969	-0.0366	0.0109	0.2212	-0.0658	0.2464	0.0237	0.0197	0.2541	-0.038	0.1874	35.596	41.8556	52.0168
4	0.616	0.4339	-0.2649	0.7985	-0.1816	3.0124	0.1443	0.2196	-0.0138	-0.3201	-0.0338	-0.054	-0.1019	-0.01	-0.1017	0.2846	0.0495	0.0121	0.2418	-0.0117	0.1772	30.9621	42.6434	49.3836
5	1.7384	-0.4337	0.6594	2.2836	0.1263	0.3513	0.287	0.3229	-0.2378	-0.8468	-0.2452	0.0255	-0.2644	-0.0373	-0.0393	0.5066	0.0574	-0.0561	0.3985	-0.0726	0.1438	29.0921	39.6585	40.6793
6	0.1963	0.3591	0.1091	1.4725	-0.5365	2.4846	0.0509	-0.0517	-0.1006	0.0296	0.1309	0.2633	0.3074	-0.8476	-0.195	0.2137	-0.0432	-0.0054	0.3666	0.0533	0.2294	17.7816	39.0341	61.4608
7	1.4411	0.0467	-0.2615	0.397	1.0058	2.5863	0.0994	0.0904	-0.6222	0.0774	-0.1674	0.3529	0.7931	-0.3061	0.0446	0.5328	-0.0345	-0.0768	0.299	-0.0938	0.3478	25.0236	28.3621	49.6298
8	0.8897	-0.6994	0.4744	0.5665	-0.45	1.8994	0.073	0.0338	-0.0188	-0.215	-0.1097	-0.0793	-0.0375	-0.061	0.0344	0.2068	-0.0157	0.0219	0.1611	0.0042	0.1668	32.3808	40.7215	67.1621
9	0.3567	-0.6779	0.3694	1.2137	-0.1026	0.7237	0.2052	0.0525	-0.1287	-0.1611	-0.108	0.1903	-0.0265	-0.1567	-0.0831	0.1938	0.0486	-0.0062	0.2174	0.0077	0.1771	20.1708	46.9107	70.0955
10	2.2007	-0.935	-0.4127	0.8905	0.2758	1.1051	0.1604	0.0608	0.2455	-0.0254	-0.0051	0.0615	-0.1188	-0.0892	-0.1351	0.2303	0.0165	0.005	0.1633	0.0187	0.186	28.688	49.9657	83.6307
11	1.936	0.104	0.7848	1.377	1.9685	3.2161	-0.0892	-0.4336	0.6121	0.0709	0.1799	-0.2384	-0.4976	0.0533	-0.0491	0.3137	-0.0564	-0.0004	0.269	-0.0978	0.3351	34.8203	56.9245	95.3362
12	0.8462	1.0119	-0.2914	1.4656	-0.7168	1.0234	-0.0841	-0.0638	0.0417	0.1451	-0.0117	0.0179	0.0057	-0.0144	0.0699	0.1819	0.0102	-0.0224	0.1541	-0.0076	0.1624	30.8236	45.6364	86.4397
13	0.4485	0.0056	-0.0522	0.8493	-0.095	1.2026	-0.0253	0.0184	-0.0556	-0.1382	0.0689	-0.2553	0.06	0.1093	-0.0397	0.1384	0.0099	0.0106	0.1778	0.01	0.1949	38.5978	40.9191	72.4012
14	0.5011	0.0765	-0.2082	1.2017	-0.4197	0.4993	0.0783	-0.0851	-0.0937	-0.2268	-0.0604	-0.2048	-0.0179	0.0154	-0.0207	0.2214	-0.0174	-0.0029	0.218	0.0099	0.2204	31.416	32.8654	70.7582
15	0.4339	-0.4261	-0.4301	2.489	0.3252	0.5518	-0.0126	0.1176	-0.1914	-0.1387	-0.1022	0.9722	0.0026	-0.4084	0.0863	0.1208	-0.0036	-0.0425	0.2549	0.0216	0.3805	10.597	26.52	82.3352
16	0.7393	-0.1209	-0.0719	2.1482	-0.3878	0.8621	-0.0379	-0.039	-0.0309	0.1682	0.0706	0.0267	-0.0774	0.0173	-0.0295	0.1422	-0.0135	-0.0109	0.1625	0.0163	0.1703	29.1142	27.7118	87.4702
17	0.7023	0.7617	-0.3487	1.348	-0.9799	0.9019	0.1352	-0.2533	0.0652	0.5592	-0.1241	0.1471	-0.1879	-0.011	-0.0441	0.2608	0.011	0.0563	0.2286	-0.0126	0.1767	22.2245	39.0972	99.5794
18	0.2559	-0.3408	-0.3125	2.7486	-0.4362	1.5404	0.0339	0.0739	-0.1231	-0.0454	-0.0658	-0.3633	0.0735	0.1696	0.035	0.0996	-0.0096	-0.0215	0.1381	0.0121	0.2187	37.8349	16.2675	84.7785
19	0.6114	-0.4194	-0.1376	1.7804	-0.4521	0.8393	0.0232	-0.0995	-0.0802	0.1969	0.0237	0.0652	-0.0289	-0.0222	-0.0281	0.1538	-0.0271	0.001	0.1881	0.0267	0.2074	26.3362	22.6985	90.5628
20	1.0959	0.4754	-0.9586	0.3361	-0.7411	1.2274	-0.2208	0.0015	-0.3532	-0.0167	0.1143	0.3088	0.3352	-0.1003	0.0589	0.2071	-0.0212	0.0158	0.2021	0.0341	0.3402	24.2996	10.3071	87.1693

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 5:22)	A	5 - 22
2	X-RAY DIFFRACTION	2	(chain A and resid 23:93)	A	23 - 93
3	X-RAY DIFFRACTION	3	(chain A and resid 94:121)	A	94 - 121
4	X-RAY DIFFRACTION	4	(chain A and resid 122:171)	A	122 - 171
5	X-RAY DIFFRACTION	5	(chain A and resid 172:189)	A	172 - 189
6	X-RAY DIFFRACTION	6	(chain A and resid 190:209)	A	190 - 209
7	X-RAY DIFFRACTION	7	(chain A and resid 210:252)	A	210 - 252
8	X-RAY DIFFRACTION	8	(chain A and resid 253:274)	A	253 - 274
9	X-RAY DIFFRACTION	9	(chain A and resid 275:295)	A	275 - 295
10	X-RAY DIFFRACTION	10	(chain A and resid 296:320)	A	296 - 320
11	X-RAY DIFFRACTION	11	(chain A and resid 321:340)	A	321 - 340
12	X-RAY DIFFRACTION	12	(chain A and resid 341:371)	A	341 - 371
13	X-RAY DIFFRACTION	13	(chain A and resid 372:398)	A	372 - 398
14	X-RAY DIFFRACTION	14	(chain A and resid 399:422)	A	399 - 422
15	X-RAY DIFFRACTION	15	(chain A and resid 423:451)	A	423 - 451
16	X-RAY DIFFRACTION	16	(chain A and resid 452:503)	A	452 - 503
17	X-RAY DIFFRACTION	17	(chain A and resid 504:529)	A	504 - 529
18	X-RAY DIFFRACTION	18	(chain A and resid 530:565)	A	530 - 565
19	X-RAY DIFFRACTION	19	(chain A and resid 566:615)	A	566 - 615
20	X-RAY DIFFRACTION	20	(chain A and resid 616:630)	A	616 - 630

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