PDB-2q5t: Full-length Cholix toxin from Vibrio Cholerae

ID or keywords:

Entry

Database: PDB / ID: 2q5t

Title

Full-length Cholix toxin from Vibrio Cholerae

Components

Cholix toxin

Pseudomonas exotoxin

Keywords

TOXIN / Domain I (Receptor binding domain) /

Beta Barrel / Domain II (Translocation domain) / six alpha-helix bundle / Domain III (catalytic domain) /

alpha-beta complex

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 /

MOLECULAR REPLACEMENT / Resolution: 2.1 Å

Authors

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

Citation

Journal: J.Biol.Chem. / Year: 2008
Title: Cholix Toxin, a Novel ADP-ribosylating Factor from Vibrio cholerae.
Authors: Jorgensen, R. / Purdy, A.E. / Fieldhouse, R.J. / Kimber, M.S. / Bartlett, D.H. / Merrill, A.R.

History

Deposition	Jun 1, 2007	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Feb 12, 2008	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.2	Aug 30, 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 / software / 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 / _software.name / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	2q5t.cif.gz	145.1 KB	Display	PDBx/mmCIF format
PDB format	pdb2q5t.ent.gz	112.3 KB	Display	PDB format
PDBx/mmJSON format	2q5t.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/q5/2q5t ftp://data.pdbj.org/pub/pdb/validation_reports/q5/2q5t	HTTPS FTP

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Related structure data

Related structure data	2q6mC 1ikqS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	6ct6-d 6mrh-1 5sy2-d 3ly8-1 6r39-1 3o3m-1 6tbf-5 6cqe-d 6irv-1 4ryc-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
Related items in Molecule of the Month	#69 - Sep 2005 Cholera Toxin similarity (1)

Deposited unit

A: Cholix toxin

hetero molecules

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

1

Idetical with deposited unit
defined by author

Unit cell

Length a, b, c (Å)	50.936, 88.338, 79.934
Angle α, β, γ (deg.)	90.00, 95.32, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Cholix toxin / Pseudomonas exotoxin Mass: 71872.984 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vibrio cholerae (bacteria) / Strain: TP / Gene: toxA / Plasmid: pET28a+ / Production host: Escherichia coli (E. coli) / Strain (production host): ER2566 / References: UniProt: Q5EK40
#2: Chemical	ChemComp-CL / CHLORIDE ION / Chloride Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C₂H₆O₂
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 406 / 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: 2.49 Å³/Da / Density % sol: 50.61 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 23% PEG 10.000, 7.5% Ethylene Glycol, 0.1 M Hepes, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: ROTATING ANODE / Type: ENRAF-NONIUS FR571 / Wavelength: 1.5418 Å
Detector	Type: Bruker Platinum 135 / Detector: CCD / Date: Feb 14, 2007
Radiation	Monochromator: Montel 200 multilayer optics / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.5418 Å / Relative weight: 1
Reflection	Resolution: 2.05→50 Å / Num. all: 44284 / Num. obs: 43440 / % possible obs: 98.1 % / Observed criterion σ(I): 0 / Redundancy: 3.9 % / R_sym value: 0.0944 / Net I/σ(I): 8.62
Reflection shell	Resolution: 2.05→2.15 Å / Redundancy: 1.97 % / Mean I/σ(I) obs: 1.31 / R_sym value: 0.5151 / % possible all: 88.8

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Phasing

Phasing MR

	Highest resolution	Lowest resolution
Rotation	3.5 Å	29.99 Å
Translation	3.5 Å	29.99 Å

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Processing

Software

Name	Version	Classification
SAINT		data scaling
PHASER		phasing
REFMAC	5.2.0019	refinement
PDB_EXTRACT	2	data extraction
PROTEUM2		data collection
PROTEUM2		data reduction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: Domain I and II of Pseudomonas exotoxin A - PDB entry 1IKQ. Domain III (the catalytic fragment of Cholix - PDB ENTRY ?)

1ikq

Resolution: 2.1→33.31 Å / Cor.coef. F_o:F_c: 0.949 / Cor.coef. F_o:F_c free: 0.921 / SU B: 10.287 / SU ML: 0.145 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / ESU R: 0.223 / ESU R Free: 0.189 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.23925	2059	5 %	RANDOM
R_work	0.19128	-	-	-
obs	0.19371	38766	99.09 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 16.914 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.1 Å²	0 Å²	-0.04 Å²
2-	-	-0.14 Å²	0 Å²
3-	-	-	0.04 Å²

Refinement step

Cycle: LAST / Resolution: 2.1→33.31 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4745	0	38	406	5189

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.008	0.022	4958
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.031	1.947	6751
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.18	5	625
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	36.883	24.256	242
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	16.544	15	811
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	17.641	15	37
X-RAY DIFFRACTION	r_chiral_restr	0.076	0.2	751
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.02	3822
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined	0.198	0.2	2196
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined	0.301	0.2	3351
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.128	0.2	419
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.252	0.2	60
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.186	0.2	21
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	0.474	1.5	3126
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	0.81	2	4974
X-RAY DIFFRACTION	r_scbond_it	1.292	3	2047
X-RAY DIFFRACTION	r_scangle_it	2.01	4.5	1766
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 2.1→2.154 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.318	134	-
R_work	0.263	2683	-
obs	-	-	93.19 %

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	10.9143	-5.1079	2.5809	3.0767	0.5879	5.3092	0.0347	1.3882	0.5777	-2.0564	-0.1798	0.3303	-1.1025	0.0959	0.1451	0.4513	0.1399	0.1183	0.1972	-0.0501	-0.2582	33.457	44.655	32.141
2	4.365	-0.8505	-1.534	3.686	0.658	4.0887	0.3081	0.2544	-0.0611	-0.8677	-0.0794	-0.4009	-0.177	0.3152	-0.2287	0.0872	-0.0046	0.0484	-0.0194	-0.0392	-0.2218	36.729	41.986	44.143
3	8.0905	-1.3672	-1.5246	2.6028	1.3263	3.644	0.1716	0.1459	-0.0698	-0.313	0.0108	-0.1302	-0.1543	0.2645	-0.1824	0.049	-0.0072	0.0568	-0.0557	0.0066	-0.1837	35.604	41.278	51.634
4	2.5397	-1.2696	-1.7167	4.0551	0.8225	4.6226	0.1647	0.3064	-0.1243	-0.5282	-0.0346	0.0846	-0.1441	-0.0423	-0.1301	-0.0021	-0.0074	-0.0196	0.0126	-0.0512	-0.1391	30.907	42.199	49.008
5	13.3125	-2.6697	-5.2989	4.747	2.5297	6.8036	0.4722	0.4927	-0.4437	-0.9914	-0.4012	0.0675	-0.4379	0.1081	-0.071	0.1429	0.107	-0.1016	-0.1524	-0.0295	-0.2659	29.393	39.315	40.229
6	4.4179	-2.3433	-0.8417	5.3598	-0.7952	7.8993	-0.208	-0.0855	-0.1904	-0.0275	0.2147	0.63	0.2539	-0.6246	-0.0067	-0.0484	-0.0345	-0.0671	0.0117	0.0315	0.0333	19.247	38.367	61.135
7	4.6295	-2.8739	4.2498	6.0548	-3.5465	10.9415	0.2928	-0.1036	-0.755	-0.3815	-0.1343	0.5845	1.142	-0.7953	-0.1585	0.2714	-0.0951	-0.1024	0.0524	-0.1032	0.0924	24.898	27.89	48.761
8	0.3918	0.348	-0.0055	2.7206	-1.5948	5.2793	0.0579	0.0917	-0.0053	-0.3084	-0.044	-0.0749	-0.0385	-0.0235	-0.0139	-0.1115	0.007	-0.0056	-0.0142	-0.0329	-0.0086	31.973	40.137	66.59
9	0.3245	-0.291	0.5133	0.3563	0.0378	3.4168	-0.0006	-0.0387	-0.1832	-0.0863	0.1772	0.1851	-0.1906	-0.2785	-0.1766	-0.0143	0.055	0.0065	0.0725	0.0263	0.0443	19.817	46.429	69.532
10	11.5104	0.8595	1.8816	2.2766	0.3097	3.3159	0.159	-0.1874	0.744	0.0827	-0.0011	0.1263	-0.3867	-0.1771	-0.1579	0.0502	0.0314	0.0856	-0.052	-0.0063	-0.0537	29.205	49.918	83.094
11	11.5829	1.124	-4.4138	20.0846	0.8319	13.2985	0.8011	-1.5951	1.426	0.823	0.018	-0.0888	-1.3504	1.0676	-0.8191	0.1758	-0.2166	0.226	0.1071	-0.3618	0.0956	34.042	56.679	94.429
12	6.2518	-0.0195	-2.9754	1.8903	-0.7276	3.0985	0.01	-0.2665	0.3169	0.3251	0.1057	0.0781	-0.1193	-0.0385	-0.1157	0.0228	0.0111	0.0035	-0.0045	-0.0185	-0.0217	30.811	45.168	85.519
13	0.9451	0.6504	0.1341	1.4992	-0.6331	0.8189	-0.0718	0.1603	0.0475	0.05	0.1735	0.0008	0.1138	0.1559	-0.1017	-0.029	0.0179	0.009	0.0131	-0.0179	-0.0031	38.362	40.621	72.068
14	5.3572	2.571	-2.2302	4.0711	-2.5442	2.1775	-0.0818	0.27	-0.3442	-0.2945	0.1268	-0.2875	0.1802	-0.1324	-0.045	-0.0183	-0.0085	-0.0217	0.0059	0.001	-0.0612	30.926	32.294	70.326
15	3.4867	-1.9966	-1.7104	6.6953	2.1541	3.7517	0.0267	0.237	-0.2316	-0.1755	0.1134	1.0009	0.0389	-0.7078	-0.1401	-0.2048	-0.0055	-0.0418	0.1604	0.1917	0.2164	10.479	25.835	81.927
16	1.2185	0.1595	-0.3503	3.2155	-0.9229	1.2552	-0.0524	-0.1244	-0.1337	0.2684	0.1684	0.2124	-0.1464	-0.1168	-0.116	-0.0658	0.0183	0.019	0.0129	0.0454	-0.041	28.533	27.361	87.319
17	0.7862	1.5816	1.0701	5.0221	0.3768	4.7921	0.0442	-0.3854	0.0169	0.7964	0.0898	0.2694	-0.5249	-0.1289	-0.1339	0.1264	0.0806	0.138	0.1703	0.0369	0.0052	21.87	39.008	99.019
18	2.6042	-1.0029	0.153	3.8361	-0.7412	1.3713	0.0187	0.0026	-0.1511	0.0565	0.0586	-0.3052	0.0755	0.0048	-0.0773	-0.105	0.0074	-0.006	-0.0021	0.0115	0.0553	37.513	16.17	84.705
19	1.9576	-0.757	-0.3999	3.0506	-0.6622	1.8429	0.0524	-0.2775	-0.121	0.2981	0.197	0.2147	-0.1038	-0.1079	-0.2493	-0.0718	0.0027	-0.0035	0.0322	0.08	-0.0048	26.005	22.62	90.196
20	13.1995	-6.3842	-3.673	5.6829	0.1159	2.9996	-0.1388	-0.0743	-1.008	0.1581	0.2824	0.7467	0.2907	-0.3273	-0.1436	-0.0491	-0.0638	-0.0212	0.0462	0.1034	0.1191	24.129	10.136	86.899

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	X-RAY DIFFRACTION	1	A	A	5 - 22	13 - 30
2	X-RAY DIFFRACTION	2	A	A	23 - 93	31 - 101
3	X-RAY DIFFRACTION	3	A	A	94 - 121	102 - 129
4	X-RAY DIFFRACTION	4	A	A	122 - 171	130 - 179
5	X-RAY DIFFRACTION	5	A	A	172 - 189	180 - 197
6	X-RAY DIFFRACTION	6	A	A	193 - 209	201 - 217
7	X-RAY DIFFRACTION	7	A	A	210 - 252	218 - 260
8	X-RAY DIFFRACTION	8	A	A	253 - 274	261 - 282
9	X-RAY DIFFRACTION	9	A	A	275 - 295	283 - 303
10	X-RAY DIFFRACTION	10	A	A	296 - 320	304 - 328
11	X-RAY DIFFRACTION	11	A	A	321 - 340	329 - 348
12	X-RAY DIFFRACTION	12	A	A	341 - 371	349 - 379
13	X-RAY DIFFRACTION	13	A	A	372 - 398	380 - 406
14	X-RAY DIFFRACTION	14	A	A	399 - 422	407 - 430
15	X-RAY DIFFRACTION	15	A	A	423 - 451	431 - 459
16	X-RAY DIFFRACTION	16	A	A	452 - 503	460 - 511
17	X-RAY DIFFRACTION	17	A	A	504 - 529	512 - 537
18	X-RAY DIFFRACTION	18	A	A	530 - 565	538 - 573
19	X-RAY DIFFRACTION	19	A	A	566 - 615	574 - 623
20	X-RAY DIFFRACTION	20	A	A	616 - 630	624 - 638

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