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- PDB-5lzj: Cholera toxin El Tor B-pentamer in complex with inhibitor Laura237 -

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Basic information

Entry
Database: PDB / ID: 5lzj
TitleCholera toxin El Tor B-pentamer in complex with inhibitor Laura237
ComponentsCholera enterotoxin subunit B
KeywordsTOXIN / cholera toxin B-pentamer / inhibitor
Function / homology
Function and homology information


host cell surface binding / galactose binding / catalytic complex / positive regulation of tyrosine phosphorylation of STAT protein / toxin activity / periplasmic space / host cell plasma membrane / extracellular region / membrane
Similarity search - Function
Heat-labile enterotoxin, B chain / Heat-labile enterotoxin beta chain / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #110 / Enterotoxin / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Chem-7BT / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Cholera enterotoxin subunit B
Similarity search - Component
Biological speciesVibrio cholerae serotype O1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsHeggelund, J.E. / Krengel, U.
CitationJournal: Sci Rep / Year: 2017
Title: Towards new cholera prophylactics and treatment: Crystal structures of bacterial enterotoxins in complex with GM1 mimics.
Authors: Heggelund, J.E. / Mackenzie, A. / Martinsen, T. / Benjamin Heim, J. / Cheshev, P. / Bernardi, A. / Krengel, U.
History
DepositionSep 29, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 31, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 7, 2017Group: Database references
Revision 1.2Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cholera enterotoxin subunit B
B: Cholera enterotoxin subunit B
C: Cholera enterotoxin subunit B
D: Cholera enterotoxin subunit B
E: Cholera enterotoxin subunit B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,76512
Polymers58,3025
Non-polymers1,4647
Water9,890549
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13810 Å2
ΔGint-44 kcal/mol
Surface area21340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.245, 66.476, 82.401
Angle α, β, γ (deg.)90.00, 116.96, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 5 molecules ABCDE

#1: Protein
Cholera enterotoxin subunit B / Cholera enterotoxin B chain / Cholera enterotoxin gamma chain / Choleragenoid


Mass: 11660.348 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961) (bacteria)
Gene: ctxB, toxB, VC_1456 / Production host: Vibrio sp. (bacteria) / References: UniProt: P01556

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Non-polymers , 5 types, 556 molecules

#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: SO4
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#5: Chemical ChemComp-7BT / (~{Z})-~{N}-[2-[(2~{R},3~{R},4~{R},5~{R},6~{R})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]ethyl]-3-(3,4,5-trimethoxyphenyl)prop-2-enamide / Laura237


Mass: 427.446 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H29NO9
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 549 / 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: 2.14 Å3/Da / Density % sol: 42.54 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1M MES pH 6, 30% PEG 400, 3% PGA-LM

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97239 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 20, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97239 Å / Relative weight: 1
ReflectionResolution: 1.2→45.6 Å / Num. obs: 144269 / % possible obs: 93.8 % / Redundancy: 2.9 % / CC1/2: 0.994 / Rmerge(I) obs: 0.096 / Net I/σ(I): 5.55
Reflection shellResolution: 1.2→1.27 Å / Redundancy: 2.3 % / CC1/2: 0.337 / % possible all: 72.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3CHB

3chb


Resolution: 1.2→73.45 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.951 / SU B: 1.441 / SU ML: 0.058 / Cross valid method: THROUGHOUT / ESU R: 0.05 / ESU R Free: 0.054 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22817 7295 5.1 %RANDOM
Rwork0.19506 ---
obs0.19671 136978 93.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.371 Å2
Baniso -1Baniso -2Baniso -3
1--0.84 Å20 Å20.02 Å2
2---0.64 Å20 Å2
3---0.96 Å2
Refinement stepCycle: 1 / Resolution: 1.2→73.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4085 0 99 549 4733
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.024444
X-RAY DIFFRACTIONr_bond_other_d0.0030.024378
X-RAY DIFFRACTIONr_angle_refined_deg2.1541.9666027
X-RAY DIFFRACTIONr_angle_other_deg1.1443.00410142
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0945566
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.16925.567194
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.4115849
X-RAY DIFFRACTIONr_dihedral_angle_4_deg26.3491515
X-RAY DIFFRACTIONr_chiral_restr0.1290.2693
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.024915
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02964
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.7641.4892111
X-RAY DIFFRACTIONr_mcbond_other1.7531.4872110
X-RAY DIFFRACTIONr_mcangle_it2.6812.2252644
X-RAY DIFFRACTIONr_mcangle_other2.6812.2262645
X-RAY DIFFRACTIONr_scbond_it2.3951.8312333
X-RAY DIFFRACTIONr_scbond_other2.3921.8312329
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.6662.6353350
X-RAY DIFFRACTIONr_long_range_B_refined5.34219.0365086
X-RAY DIFFRACTIONr_long_range_B_other5.34119.0345086
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.199→1.231 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.397 360 -
Rwork0.383 6801 -
obs--63.23 %

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