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- PDB-1s5e: Cholera holotoxin, Crystal form 1 -

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Basic information

Entry
Database: PDB / ID: 1s5e
TitleCholera holotoxin, Crystal form 1
Components
  • Cholera enterotoxin, A chain precursor
  • cholera toxin B protein (CTB)
KeywordsTRANSFERASE / TOXIN / cholera toxin / heat-labile enterotoxin / ADP ribose transferases / AB5 toxins
Function / homology
Function and homology information


host cell surface binding / galactose binding / glycosyltransferase activity / catalytic complex / Transferases; Glycosyltransferases; Pentosyltransferases / localization / positive regulation of tyrosine phosphorylation of STAT protein / nucleotidyltransferase activity / toxin activity / periplasmic space ...host cell surface binding / galactose binding / glycosyltransferase activity / catalytic complex / Transferases; Glycosyltransferases; Pentosyltransferases / localization / positive regulation of tyrosine phosphorylation of STAT protein / nucleotidyltransferase activity / toxin activity / periplasmic space / lipid binding / host cell plasma membrane / extracellular space / extracellular region / membrane
Similarity search - Function
Heat-labile enterotoxin, A chain / Heat-labile enterotoxin alpha chain / Heat-Labile Enterotoxin; Chain A / Heat-Labile Enterotoxin, subunit A / Heat-labile enterotoxin, B chain / Heat-labile enterotoxin beta chain / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #110 / Enterotoxin / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Alpha-Beta Complex ...Heat-labile enterotoxin, A chain / Heat-labile enterotoxin alpha chain / Heat-Labile Enterotoxin; Chain A / Heat-Labile Enterotoxin, subunit A / Heat-labile enterotoxin, B chain / Heat-labile enterotoxin beta chain / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #110 / Enterotoxin / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Alpha-Beta Complex / Beta Barrel / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
beta-D-galactopyranose / Cholera enterotoxin subunit A / Cholera enterotoxin subunit B
Similarity search - Component
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsO'Neal, C.J. / Amaya, E.I. / Jobling, M.G. / Holmes, R.K. / Hol, W.G.
CitationJournal: 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
DepositionJan 20, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 6, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.3Jul 29, 2020Group: 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 1.4Aug 23, 2023Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)171,09716
Polymers170,69112
Non-polymers4064
Water13,475748
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


Theoretical massNumber of molelcules
Total (without water)85,5488
Polymers85,3456
Non-polymers2032
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16680 Å2
ΔGint-69 kcal/mol
Surface area28020 Å2
MethodPISA
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


Theoretical massNumber of molelcules
Total (without water)85,5488
Polymers85,3456
Non-polymers2032
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16830 Å2
ΔGint-65 kcal/mol
Surface area27580 Å2
MethodPISA
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 number4
Space group name H-MP1211

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Components

#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 / Galactose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGalpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-galactopyranoseCOMMON NAMEGMML 1.0
b-D-GalpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GalSNFG CARBOHYDRATE SYMBOLGMML 1.0
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 748 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.42 Å3/Da / Density % sol: 48.86 %
Crystal growTemperature: 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

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1.0781 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 24, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0781 Å / Relative weight: 1
ReflectionResolution: 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 % / Rsym value: 0.083 / Net I/σ(I): 14.5
Reflection shellResolution: 1.9→1.97 Å / Mean I/σ(I) obs: 2.85 / Num. unique all: 11923 / Rsym value: 0.391 / % possible all: 97.1

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: CTY30S Form 3 structure (PDB ID 1S5B)

1s5b


Resolution: 1.9→40.82 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc 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
RfactorNum. reflection% reflectionSelection details
Rfree0.20521 6126 5 %RANDOM
Rwork0.16716 ---
all0.16904 116190 --
obs0.16904 116190 98.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 13.109 Å2
Baniso -1Baniso -2Baniso -3
1--0.05 Å20 Å2-0.13 Å2
2--0.14 Å20 Å2
3----0.11 Å2
Refinement stepCycle: LAST / Resolution: 1.9→40.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11664 0 26 748 12438
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.02111939
X-RAY DIFFRACTIONr_bond_other_d0.0010.0210434
X-RAY DIFFRACTIONr_angle_refined_deg1.411.9316183
X-RAY DIFFRACTIONr_angle_other_deg0.787324337
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.53151473
X-RAY DIFFRACTIONr_chiral_restr0.1040.21804
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213319
X-RAY DIFFRACTIONr_gen_planes_other0.0070.022323
X-RAY DIFFRACTIONr_nbd_refined0.2170.32252
X-RAY DIFFRACTIONr_nbd_other0.2670.311932
X-RAY DIFFRACTIONr_nbtor_other0.090.56786
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.170.51297
X-RAY DIFFRACTIONr_metal_ion_refined0.120.55
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2670.316
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3710.375
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1580.527
X-RAY DIFFRACTIONr_mcbond_it1.15727409
X-RAY DIFFRACTIONr_mcangle_it1.874311945
X-RAY DIFFRACTIONr_scbond_it1.44724530
X-RAY DIFFRACTIONr_scangle_it2.334238
LS refinement shellResolution: 1.9→1.944 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.267 440
Rwork0.231 8128
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°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)
11.80670.13120.63591.4120.64782.30270.09430.0835-0.2063-0.07450.0252-0.11620.26710.2322-0.11950.18850.02340.04070.1281-0.02020.20062.219-18.36439.701
22.16631.85033.44652.38583.7355.7476-0.07860.19790.0215-0.04550.0885-0.1166-0.01740.2106-0.00990.2045-0.02840.04860.18110.00250.20138.98-2.76338.036
31.2182-0.2617-0.06210.7473-0.22690.8522-0.02820.0724-0.1167-0.04-0.0303-0.0840.04770.0560.05850.1927-0.00240.03520.1218-0.01090.232233.451-2.52642.224
41.3906-0.4164-0.39951.76070.11690.77390.0610.16720.0754-0.1287-0.0263-0.0664-0.0614-0.0932-0.03470.20720.010.03150.15020.0220.173821.07114.65136.502
51.1349-0.183-0.55580.7880.01291.15980.07730.04230.1176-0.0284-0.01910.1119-0.148-0.0834-0.05820.20410.01640.02880.1258-0.00660.2298.11119.66353.655
61.4019-0.1792-0.21121.3685-0.06181.0624-0.0686-0.3068-0.02780.15040.0260.05590.01770.0150.04260.20860.01230.03530.18230.01160.174612.7185.50969.711
71.9463-0.099-0.44960.73860.26930.9734-0.1182-0.2842-0.26640.05080.0384-0.02040.06090.07840.07980.08880.03020.02770.0420.07060.126428.248-8.29662.674
81.5044-0.0579-0.01971.10170.06731.11410.02460.0624-0.13680.0179-0.02880.06150.09960.04330.00420.1596-0.0010.04160.1177-0.03640.234238.12730.1978.288
93.78033.43573.30464.834.05473.9229-0.02670.2553-0.0186-0.0730.0983-0.1264-0.00820.0873-0.07160.15820.00030.05760.1679-0.01520.207950.10343.1273.202
101.5445-0.472-0.11860.833-0.32531.27120.02430.1444-0.0725-0.0191-0.0472-0.04040.00690.02870.02290.1821-0.00230.02250.1491-0.02350.213175.18844.5167.437
112.3992-0.3519-0.22491.57710.30240.84860.15670.3890.2155-0.171-0.1707-0.0317-0.0916-0.0910.0140.19050.05080.03510.19830.04320.187163.11159.96-2.245
121.6917-0.7528-0.25651.8390.13290.89760.07280.09890.2536-0.0806-0.07430.1409-0.1348-0.06360.00150.170.01450.03320.1076-0.01920.285649.90368.88813.018
131.4422-0.47010.06271.5424-0.08751.2603-0.0548-0.2720.1420.24140.08560.119-0.0322-0.0499-0.03090.20830.00340.06580.1653-0.05370.225554.02458.72532.079
142.0037-0.337-0.33111.0670.23290.8634-0.0578-0.2646-0.04290.15210.0410.02270.04370.04370.01690.21350.00150.01730.14930.0070.18969.69343.7828.757
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 49
2X-RAY DIFFRACTION2A197 - 236
3X-RAY DIFFRACTION3D1 - 103
4X-RAY DIFFRACTION4E1 - 103
5X-RAY DIFFRACTION5F1 - 103
6X-RAY DIFFRACTION6G1 - 102
7X-RAY DIFFRACTION7H1 - 103
8X-RAY DIFFRACTION8B1 - 189
9X-RAY DIFFRACTION9B198 - 235
10X-RAY DIFFRACTION10J1 - 103
11X-RAY DIFFRACTION11K1 - 103
12X-RAY DIFFRACTION12L1 - 103
13X-RAY DIFFRACTION13M1 - 103
14X-RAY DIFFRACTION14N1 - 103

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