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- PDB-1s5c: Cholera holotoxin with an A-subunit Y30S mutation, Crystal form 1 -

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Basic information

Entry
Database: PDB / ID: 1s5c
TitleCholera holotoxin with an A-subunit Y30S mutation, Crystal form 1
Components
  • Cholera enterotoxin, A chain
  • cholera enterotoxin B-subunit
KeywordsTRANSFERASE / TOXIN / cholera toxin / heat-labile enterotoxin / ADP ribose transferases / AB5 toxins
Function / homology
Function and homology information


symbiont-mediated activation of host G protein-coupled receptor signal transduction / 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 ...symbiont-mediated activation of host G protein-coupled receptor signal transduction / 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 / 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
Cholera enterotoxin subunit A / Cholera enterotoxin subunit B
Similarity search - Component
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 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 / Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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_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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 23, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cholera enterotoxin, A chain
D: cholera enterotoxin B-subunit
E: cholera enterotoxin B-subunit
F: cholera enterotoxin B-subunit
G: cholera enterotoxin B-subunit
H: cholera enterotoxin B-subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,2927
Polymers85,2696
Non-polymers231
Water1,69394
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15600 Å2
ΔGint-70 kcal/mol
Surface area27410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.818, 85.199, 71.255
Angle α, β, γ (deg.)90.00, 104.48, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Cholera enterotoxin, A chain / NAD(+)--diphthamide ADP- ribosyltransferase / Cholera enterotoxin A subunit


Mass: 27152.875 Da / Num. of mol.: 1 / Mutation: Y30S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria) / Gene: CTXA, TOXA, VC1457 / Plasmid: pEIA154 / 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 enterotoxin B-subunit


Mass: 11623.267 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria) / Gene: CTXB, TOXB, VC1456 / Plasmid: pEIA154 / 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.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 94 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.2 Å3/Da / Density % sol: 43.65 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: PEG 2000mme, MES, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 1.0414 Å
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Apr 24, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0414 Å / Relative weight: 1
ReflectionResolution: 2.5→19.96 Å / Num. all: 23503 / Num. obs: 23503 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Rsym value: 0.106 / Net I/σ(I): 12.2
Reflection shellResolution: 2.5→2.59 Å / Mean I/σ(I) obs: 2.5 / Num. unique all: 2357 / Rsym value: 0.484 / % possible all: 98.7

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 1LTG, 3CHB

1ltg

3chb


Resolution: 2.5→19.96 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.885 / SU B: 11.12 / SU ML: 0.248 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.338 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26172 1208 5.1 %RANDOM
Rwork0.19542 ---
all0.19882 22291 --
obs0.19882 22291 98.89 %-
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: 16.802 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å2-0.04 Å2
2---0.01 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.5→19.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5612 0 1 94 5707
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0215734
X-RAY DIFFRACTIONr_bond_other_d0.0030.024973
X-RAY DIFFRACTIONr_angle_refined_deg1.2151.9287784
X-RAY DIFFRACTIONr_angle_other_deg0.873311565
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8775722
X-RAY DIFFRACTIONr_chiral_restr0.070.2868
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.026470
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021114
X-RAY DIFFRACTIONr_nbd_refined0.1760.31194
X-RAY DIFFRACTIONr_nbd_other0.1950.35920
X-RAY DIFFRACTIONr_nbtor_other0.0840.53308
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2090.5196
X-RAY DIFFRACTIONr_metal_ion_refined0.080.52
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1020.337
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1940.3105
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2450.511
X-RAY DIFFRACTIONr_mcbond_it0.86933623
X-RAY DIFFRACTIONr_mcangle_it1.42545812
X-RAY DIFFRACTIONr_scbond_it1.36542111
X-RAY DIFFRACTIONr_scangle_it2.17861972
LS refinement shellResolution: 2.5→2.56 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.297 81
Rwork0.236 1568
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)
14.85720.61031.83340.91640.39662.4556-0.02070.25430.37210.11120.15170.2376-0.19770.3746-0.1310.0677-0.030.07290.0969-0.01370.160827.509150.161837.287
2-1.2436-2.5024-2.82945.86122.13921.57580.1862-0.2391-0.03470.256-0.131-0.072-0.65540.1717-0.05520.12370.02550.02320.1825-0.04480.086322.878639.634550.2792
31.13620.8612-0.26381.0263-0.38081.4230.04610.05660.15970.12640.08930.0832-0.06570.0127-0.13550.06040.03060.03280.118-0.02080.121919.869843.426339.6357
40.99680.6897-2.90420.1139-0.87846.3171-0.0264-0.1093-0.0958-0.07380.01440.04330.09840.14080.01190.12120.07750.04270.1840.01980.097734.527332.546532.9032
51.1830.21520.99812.0059-0.71481.4382-0.0679-0.09330.0209-0.0057-0.0245-0.0609-0.00150.070.09240.06630.0118-0.00710.1164-0.01930.103559.425435.666128.1031
62.30640.59050.40721.30110.35031.74130.0972-0.1098-0.12210.00190.0245-0.04790.15690.0359-0.12170.11970.0087-0.0260.06520.03670.0847.159618.823620.8257
70.9827-0.41410.38512.4017-0.14120.53150.0042-0.02390.0718-0.1097-0.01260.07970.1098-0.01630.00840.1029-0.02950.0230.12210.00940.060833.640726.6195.5
81.5219-0.03780.53923.43720.22971.3745-0.05160.0198-0.0276-0.10780.0344-0.1904-0.0884-0.05590.01720.06490.00020.06120.10240.02190.064338.023647.90322.7548
92.2106-0.66820.94462.0199-0.23882.6727-0.23920.10980.22170.19050.0063-0.3428-0.29030.02780.23290.0908-0.0309-0.08340.01210.040.16254.227653.230516.3289
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 251 - 25
2X-RAY DIFFRACTION2AA37 - 4937 - 49
3X-RAY DIFFRACTION3AA51 - 18851 - 188
4X-RAY DIFFRACTION4AA196 - 234196 - 234
5X-RAY DIFFRACTION5DB1 - 1031 - 103
6X-RAY DIFFRACTION6EC1 - 1031 - 103
7X-RAY DIFFRACTION7FD1 - 1031 - 103
8X-RAY DIFFRACTION8GE1 - 1031 - 103
9X-RAY DIFFRACTION9HF1 - 1031 - 103

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