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- PDB-1s5b: Cholera holotoxin with an A-subunit Y30S mutation Form 3 -

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Basic information

Entry
Database: PDB / ID: 1s5b
TitleCholera holotoxin with an A-subunit Y30S mutation Form 3
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 / 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 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: 2.13 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_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 / _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 1.5Oct 30, 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 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)85,2927
Polymers85,2696
Non-polymers231
Water7,278404
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.104, 107.431, 65.950
Angle α, β, γ (deg.)90.00, 91.29, 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: 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 toxin B protein (CTB)


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.: 404 / 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: 2.69 Å3/Da / Density % sol: 53.92 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: PEG 2000mme, MES, kemptide, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Mar 17, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.13→20.02 Å / Num. all: 46304 / Num. obs: 46304 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Rsym value: 0.096 / Net I/σ(I): 12.1
Reflection shellResolution: 2.13→2.21 Å / Mean I/σ(I) obs: 3.3 / Num. unique all: 4648 / Rsym value: 0.392 / % possible all: 99.8

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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: 2.13→20.02 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.918 / SU B: 5.175 / SU ML: 0.132 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.214 / ESU R Free: 0.181 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22425 2340 5.1 %RANDOM
Rwork0.1775 ---
all0.17988 43956 --
obs0.17988 43956 99.29 %-
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: 12.395 Å2
Baniso -1Baniso -2Baniso -3
1--0.11 Å20 Å2-0.06 Å2
2--0.13 Å20 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 2.13→20.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5647 0 1 404 6052
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0215771
X-RAY DIFFRACTIONr_bond_other_d0.0010.025064
X-RAY DIFFRACTIONr_angle_refined_deg1.2821.937824
X-RAY DIFFRACTIONr_angle_other_deg0.704311807
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5465713
X-RAY DIFFRACTIONr_chiral_restr0.0760.2877
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.026428
X-RAY DIFFRACTIONr_gen_planes_other0.0040.021115
X-RAY DIFFRACTIONr_nbd_refined0.2130.31211
X-RAY DIFFRACTIONr_nbd_other0.2630.35988
X-RAY DIFFRACTIONr_nbtor_other0.090.53320
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2050.5649
X-RAY DIFFRACTIONr_metal_ion_refined0.1330.53
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1940.310
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3030.330
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2730.517
X-RAY DIFFRACTIONr_mcbond_it0.88723598
X-RAY DIFFRACTIONr_mcangle_it1.43635796
X-RAY DIFFRACTIONr_scbond_it0.9122173
X-RAY DIFFRACTIONr_scangle_it1.43232028
LS refinement shellResolution: 2.13→2.187 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.26 160
Rwork0.201 3043
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)
12.2715-0.15870.06651.63710.14212.9628-0.0203-0.318-0.60070.0774-0.05070.05310.31470.17230.07090.17620.03530.08090.09590.11810.329657.203-54.69855.396
24.7466-2.98983.67842.7617-3.16814.3377-0.2577-0.70480.21730.14410.0933-0.2369-0.09-0.44150.16440.2209-0.00560.05270.18910.00280.174344.684-40.92756.93
31.2880.5901-0.22510.8909-0.30650.2904-0.0295-0.02530.10330.1136-0.0286-0.02830.04460.04170.05810.18750.0406-0.03450.0795-0.02450.142444.858-18.84340.822
41.04570.0623-0.48610.13340.26171.2097-0.050.26420.01660.11940.01180.1212-0.1102-0.05330.03820.158-0.0195-0.02990.10270.05340.151440.572-33.44625.179
50.30120.2252-0.14751.1408-0.03550.3677-0.03020.10850.122-0.08790.01090.2121-0.0891-0.02750.01930.15650.07730.03210.10290.01080.124624.667-46.932.158
60.69270.4287-0.31480.1523-0.40561.01780.07990.01440.0828-0.1739-0.0087-0.0614-0.0616-0.1433-0.07120.16230.0112-0.05190.0553-0.01340.137819.337-40.6452.528
70.82620.277-0.14610.7970.42690.92510.0481-0.14730.0504-0.0235-0.03420.0117-0.07280.1109-0.01390.17320.00430.03220.08810.05950.145131.452-23.1857.703
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 251 - 25
2X-RAY DIFFRACTION1AA37 - 4637 - 46
3X-RAY DIFFRACTION1AA53 - 18853 - 188
4X-RAY DIFFRACTION2AA198 - 234198 - 234
5X-RAY DIFFRACTION3DB1 - 1031 - 103
6X-RAY DIFFRACTION4EC1 - 1031 - 103
7X-RAY DIFFRACTION5FD1 - 1031 - 103
8X-RAY DIFFRACTION6GE1 - 1031 - 103
9X-RAY DIFFRACTION7HF1 - 1031 - 103

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