PDB-1s5e: Cholera holotoxin, Crystal form 1

ID or keywords:

Entry

Database: PDB / ID: 1s5e

Title

Cholera holotoxin, Crystal form 1

Components

Cholera enterotoxin, A chain precursor
cholera toxin B protein (CTB)

Keywords

TRANSFERASE / TOXIN / cholera toxin / heat-labile enterotoxin / ADP ribose transferases / AB5 toxins

Function / homology

Function and homology information

host cell surface binding / galactose binding / positive regulation of tyrosine phosphorylation of STAT protein / glycosyltransferase activity / Transferases; Glycosyltransferases; Pentosyltransferases / catalytic complex / nucleotidyltransferase activity / toxin activity / periplasmic space / lipid binding ...
Similarity search - Function

Biological species

Vibrio cholerae (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.9 Å

Authors

O'Neal, C.J. / Amaya, E.I. / Jobling, M.G. / Holmes, R.K. / Hol, W.G.

Citation

Journal: Biochemistry / Year: 2004
Title: Crystal structures of an intrinsically active cholera toxin mutant yield insight into the toxin activation mechanism
Authors: O'Neal, C.J. / Amaya, E.I. / Jobling, M.G. / Holmes, R.K. / Hol, W.G.

History

Deposition	Jan 20, 2004	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Apr 6, 2004	Provider: repository / Type: Initial release
Revision 1.1	Apr 29, 2008	Group: Version format compliance
Revision 1.2	Jul 13, 2011	Group: Advisory / Refinement description / Version format compliance
Revision 1.3	Jul 29, 2020	Group: Data collection / Derived calculations / Structure summary Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4	Aug 23, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_sheet Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_sheet.number_strands
Revision 1.5	Oct 30, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	1s5e.cif.gz	310.7 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	1s5e_validation.pdf.gz	517.8 KB	Display	wwPDB validaton report
Full document	1s5e_full_validation.pdf.gz	535.4 KB	Display
Data in XML	1s5e_validation.xml.gz	59.9 KB	Display
Data in CIF	1s5e_validation.cif.gz	85 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/s5/1s5e ftp://data.pdbj.org/pub/pdb/validation_reports/s5/1s5e	HTTPS FTP

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Related structure data

Related structure data	1s5bSC 1s5cC 1s5dC 1s5fC 1lta 1ltg 1lts 1xtc S: Starting model for refinement C: citing same article (ref.)
Similar structure data	1ltt-d 1lt3-d 1s5f-d 1s5c-d 1lta-d 1lts-d 1lti-d 1lt4-d 1ltb-d 1s5b-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	#69 - Sep 2005 Cholera Toxin similarity (8) #156 - Dec 2012 ABO Blood Type Glycosyltransferases similarity (1) #198 - Jun 2016 Beta-galactosidase similarity (1)

Deposited unit

A: Cholera enterotoxin, A chain precursor

D: cholera toxin B protein (CTB)

E: cholera toxin B protein (CTB)

F: cholera toxin B protein (CTB)

G: cholera toxin B protein (CTB)

H: cholera toxin B protein (CTB)

B: Cholera enterotoxin, A chain precursor

J: cholera toxin B protein (CTB)

K: cholera toxin B protein (CTB)

L: cholera toxin B protein (CTB)

M: cholera toxin B protein (CTB)

N: cholera toxin B protein (CTB)

hetero molecules

171 kDa, 12 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Cholera enterotoxin, A chain precursor

D: cholera toxin B protein (CTB)

E: cholera toxin B protein (CTB)

F: cholera toxin B protein (CTB)

G: cholera toxin B protein (CTB)

H: cholera toxin B protein (CTB)

hetero molecules

defined by author&software
85.5 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Cholera enterotoxin, A chain precursor

J: cholera toxin B protein (CTB)

K: cholera toxin B protein (CTB)

L: cholera toxin B protein (CTB)

M: cholera toxin B protein (CTB)

N: cholera toxin B protein (CTB)

hetero molecules

defined by author&software
85.5 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	59.931, 108.230, 122.976
Angle α, β, γ (deg.)	90.00, 95.89, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein

Cholera enterotoxin, A chain precursor / NAD(+)--diphthamide ADP- ribosyltransferase / Cholera enterotoxin A subunit

Mass: 27228.971 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Vibrio cholerae (bacteria) / Gene: CTXA, TOXA, VC1457 / Plasmid: pARCT5 / Species (production host): Escherichia coli / Production host:

Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P01555, NAD+-diphthamide ADP-ribosyltransferase

#2: Protein

cholera toxin B protein (CTB)

Mass: 11623.267 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Vibrio cholerae (bacteria) / Gene: CTXB, TOXB, VC1456 / Plasmid: pARCT5 / Species (production host): Escherichia coli / Production host:

Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P01556

#3: Chemical

ChemComp-NA / SODIUM ION

Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na

#4: Sugar

ChemComp-GAL / beta-D-galactopyranose / beta-D-galactose / D-galactose / galactose

Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C₆H₁₂O₆

#5: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 748 / 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: 2.42 Å³/Da / Density % sol: 48.86 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop Details: PEG 3350, magnesium acetate, galactose, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1.0781 Å
Detector	Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 24, 2002
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.0781 Å / Relative weight: 1
Reflection	Resolution: 1.9→49.39 Å / Num. all: 122327 / Num. obs: 122327 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / R_sym value: 0.083 / Net I/σ(I): 14.5
Reflection shell	Resolution: 1.9→1.97 Å / Mean I/σ(I) obs: 2.85 / Num. unique all: 11923 / R_sym value: 0.391 / % possible all: 97.1

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Processing

Software

Name	Version	Classification
REFMAC	5.1.24	refinement
HKL-2000		data reduction
SCALEPACK		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: CTY30S Form 3 structure (PDB ID 1S5B)

1s5b

Resolution: 1.9→40.82 Å / Cor.coef. F_o:F_c: 0.963 / Cor.coef. F_o:F_c free: 0.944 / SU B: 2.95 / SU ML: 0.087 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.14 / ESU R Free: 0.13 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.20521	6126	5 %	RANDOM
R_work	0.16716	-	-	-
all	0.16904	116190	-	-
obs	0.16904	116190	98.88 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK

Displacement parameters

B_iso mean: 13.109 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.05 Å²	0 Å²	-0.13 Å²
2-	-	0.14 Å²	0 Å²
3-	-	-	-0.11 Å²

Refinement step

Cycle: LAST / Resolution: 1.9→40.82 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	11664	0	26	748	12438

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.013	0.021	11939
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	10434
X-RAY DIFFRACTION	r_angle_refined_deg	1.41	1.93	16183
X-RAY DIFFRACTION	r_angle_other_deg	0.787	3	24337
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.531	5	1473
X-RAY DIFFRACTION	r_chiral_restr	0.104	0.2	1804
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.02	13319
X-RAY DIFFRACTION	r_gen_planes_other	0.007	0.02	2323
X-RAY DIFFRACTION	r_nbd_refined	0.217	0.3	2252
X-RAY DIFFRACTION	r_nbd_other	0.267	0.3	11932
X-RAY DIFFRACTION	r_nbtor_other	0.09	0.5	6786
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.17	0.5	1297
X-RAY DIFFRACTION	r_metal_ion_refined	0.12	0.5	5
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.267	0.3	16
X-RAY DIFFRACTION	r_symmetry_vdw_other	0.371	0.3	75
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.158	0.5	27
X-RAY DIFFRACTION	r_mcbond_it	1.157	2	7409
X-RAY DIFFRACTION	r_mcangle_it	1.874	3	11945
X-RAY DIFFRACTION	r_scbond_it	1.447	2	4530
X-RAY DIFFRACTION	r_scangle_it	2.3	3	4238

LS refinement shell

Resolution: 1.9→1.944 Å / Total num. of bins used: 20 /

	R_factor	Num. reflection
R_free	0.267	440
R_work	0.231	8128

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	1.8067	0.1312	0.6359	1.412	0.6478	2.3027	0.0943	0.0835	-0.2063	-0.0745	0.0252	-0.1162	0.2671	0.2322	-0.1195	0.1885	0.0234	0.0407	0.1281	-0.0202	0.2006	2.219	-18.364	39.701
2	2.1663	1.8503	3.4465	2.3858	3.735	5.7476	-0.0786	0.1979	0.0215	-0.0455	0.0885	-0.1166	-0.0174	0.2106	-0.0099	0.2045	-0.0284	0.0486	0.1811	0.0025	0.2013	8.98	-2.763	38.036
3	1.2182	-0.2617	-0.0621	0.7473	-0.2269	0.8522	-0.0282	0.0724	-0.1167	-0.04	-0.0303	-0.084	0.0477	0.056	0.0585	0.1927	-0.0024	0.0352	0.1218	-0.0109	0.2322	33.451	-2.526	42.224
4	1.3906	-0.4164	-0.3995	1.7607	0.1169	0.7739	0.061	0.1672	0.0754	-0.1287	-0.0263	-0.0664	-0.0614	-0.0932	-0.0347	0.2072	0.01	0.0315	0.1502	0.022	0.1738	21.071	14.651	36.502
5	1.1349	-0.183	-0.5558	0.788	0.0129	1.1598	0.0773	0.0423	0.1176	-0.0284	-0.0191	0.1119	-0.148	-0.0834	-0.0582	0.2041	0.0164	0.0288	0.1258	-0.0066	0.229	8.111	19.663	53.655
6	1.4019	-0.1792	-0.2112	1.3685	-0.0618	1.0624	-0.0686	-0.3068	-0.0278	0.1504	0.026	0.0559	0.0177	0.015	0.0426	0.2086	0.0123	0.0353	0.1823	0.0116	0.1746	12.718	5.509	69.711
7	1.9463	-0.099	-0.4496	0.7386	0.2693	0.9734	-0.1182	-0.2842	-0.2664	0.0508	0.0384	-0.0204	0.0609	0.0784	0.0798	0.0888	0.0302	0.0277	0.042	0.0706	0.1264	28.248	-8.296	62.674
8	1.5044	-0.0579	-0.0197	1.1017	0.0673	1.1141	0.0246	0.0624	-0.1368	0.0179	-0.0288	0.0615	0.0996	0.0433	0.0042	0.1596	-0.001	0.0416	0.1177	-0.0364	0.2342	38.127	30.197	8.288
9	3.7803	3.4357	3.3046	4.83	4.0547	3.9229	-0.0267	0.2553	-0.0186	-0.073	0.0983	-0.1264	-0.0082	0.0873	-0.0716	0.1582	0.0003	0.0576	0.1679	-0.0152	0.2079	50.103	43.127	3.202
10	1.5445	-0.472	-0.1186	0.833	-0.3253	1.2712	0.0243	0.1444	-0.0725	-0.0191	-0.0472	-0.0404	0.0069	0.0287	0.0229	0.1821	-0.0023	0.0225	0.1491	-0.0235	0.2131	75.188	44.516	7.437
11	2.3992	-0.3519	-0.2249	1.5771	0.3024	0.8486	0.1567	0.389	0.2155	-0.171	-0.1707	-0.0317	-0.0916	-0.091	0.014	0.1905	0.0508	0.0351	0.1983	0.0432	0.1871	63.111	59.96	-2.245
12	1.6917	-0.7528	-0.2565	1.839	0.1329	0.8976	0.0728	0.0989	0.2536	-0.0806	-0.0743	0.1409	-0.1348	-0.0636	0.0015	0.17	0.0145	0.0332	0.1076	-0.0192	0.2856	49.903	68.888	13.018
13	1.4422	-0.4701	0.0627	1.5424	-0.0875	1.2603	-0.0548	-0.272	0.142	0.2414	0.0856	0.119	-0.0322	-0.0499	-0.0309	0.2083	0.0034	0.0658	0.1653	-0.0537	0.2255	54.024	58.725	32.079
14	2.0037	-0.337	-0.3311	1.067	0.2329	0.8634	-0.0578	-0.2646	-0.0429	0.1521	0.041	0.0227	0.0437	0.0437	0.0169	0.2135	0.0015	0.0173	0.1493	0.007	0.189	69.693	43.78	28.757

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	1 - 49
2	X-RAY DIFFRACTION	2	A	197 - 236
3	X-RAY DIFFRACTION	3	D	1 - 103
4	X-RAY DIFFRACTION	4	E	1 - 103
5	X-RAY DIFFRACTION	5	F	1 - 103
6	X-RAY DIFFRACTION	6	G	1 - 102
7	X-RAY DIFFRACTION	7	H	1 - 103
8	X-RAY DIFFRACTION	8	B	1 - 189
9	X-RAY DIFFRACTION	9	B	198 - 235
10	X-RAY DIFFRACTION	10	J	1 - 103
11	X-RAY DIFFRACTION	11	K	1 - 103
12	X-RAY DIFFRACTION	12	L	1 - 103
13	X-RAY DIFFRACTION	13	M	1 - 103
14	X-RAY DIFFRACTION	14	N	1 - 103

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