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- PDB-5lzg: Cholera toxin El Tor B-pentamer in complex with inhibitor PC262 -

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Basic information

Entry
Database: PDB / ID: 5lzg
TitleCholera toxin El Tor B-pentamer in complex with inhibitor PC262
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-7BN / IMIDAZOLE / DI(HYDROXYETHYL)ETHER / Cholera enterotoxin subunit B
Similarity search - Component
Biological speciesVibrio cholerae serotype O1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.13 Å
AuthorsHeggelund, J.E. / Martinsen, T. / 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)61,89415
Polymers58,3025
Non-polymers3,59310
Water10,359575
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14030 Å2
ΔGint-41 kcal/mol
Surface area20470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.880, 66.291, 77.407
Angle α, β, γ (deg.)90.00, 105.74, 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)
Strain: ATCC 39315 / El Tor Inaba N16961 / Gene: ctxB, toxB, VC_1456 / Production host: Vibrio sp. (bacteria) / References: UniProt: P01556

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Non-polymers , 6 types, 585 molecules

#2: Chemical
ChemComp-7BN / (2~{R},4~{S},5~{R},6~{R})-5-acetamido-2-[4-[3-[2-[(2~{S},3~{R},4~{R},5~{R},6~{R})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]ethylamino]-3-oxidanylidene-propyl]-1,2,3-triazol-1-yl]-4-oxidanyl-6-[(1~{R},2~{R})-1,2,3-tris(oxidanyl)propyl]oxane-2-carboxylic acid


Mass: 621.592 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C24H39N5O14
#3: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Chemical ChemComp-IMD / IMIDAZOLE / Imidazole


Mass: 69.085 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H5N2
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 575 / 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: 2.16 Å3/Da / Density % sol: 42.99 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1 M MES/Imidazole buffer, pH 6.5, 10% PEG 1000, 10 % PEG 3350, 10 % MPD, 0.03 M divalent cations

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.991872 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.991872 Å / Relative weight: 1
ReflectionResolution: 1.12→47.8 Å / Num. obs: 139423 / % possible obs: 74.3 % / Redundancy: 2.7 % / CC1/2: 0.999 / Net I/σ(I): 8.94
Reflection shellResolution: 1.12→1.19 Å / Redundancy: 1.6 % / Mean I/σ(I) obs: 0.7 / CC1/2: 0.359 / % possible all: 13.7

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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: 1.13→47.8 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.97 / SU B: 2.431 / SU ML: 0.051 / Cross valid method: THROUGHOUT / ESU R: 0.047 / ESU R Free: 0.049 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1975 6982 5 %RANDOM
Rwork0.17471 ---
obs0.17587 132437 74.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 17.565 Å2
Baniso -1Baniso -2Baniso -3
1--0.79 Å20 Å20.24 Å2
2---0.58 Å20 Å2
3---1.06 Å2
Refinement stepCycle: LAST / Resolution: 1.13→47.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4085 0 248 575 4908
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.024569
X-RAY DIFFRACTIONr_bond_other_d0.0060.024393
X-RAY DIFFRACTIONr_angle_refined_deg1.8992.0016218
X-RAY DIFFRACTIONr_angle_other_deg1.2583.01710173
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1025547
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.01625.126199
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.48515816
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.8641520
X-RAY DIFFRACTIONr_chiral_restr0.1150.2728
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.024988
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02996
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_it0.6860.8372103
X-RAY DIFFRACTIONr_mcbond_other0.6620.8342101
X-RAY DIFFRACTIONr_mcangle_it1.0881.2472632
X-RAY DIFFRACTIONr_mcangle_other1.0891.2482633
X-RAY DIFFRACTIONr_scbond_it1.0251.0922466
X-RAY DIFFRACTIONr_scbond_other1.0251.0932467
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.591.5893571
X-RAY DIFFRACTIONr_long_range_B_refined4.21312.2495237
X-RAY DIFFRACTIONr_long_range_B_other4.21312.2565238
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.125→1.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.413 33 -
Rwork0.447 783 -
obs--5.93 %
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)
10.86250.05020.21360.7113-0.05950.4998-0.08180.06580.1727-0.04730.03530.1716-0.01230.00570.04650.0362-0.0037-0.07460.03040.01610.1647-18.95084.772511.7798
21.6580.50150.21460.8164-0.09810.3917-0.1135-0.00880.4036-0.01570.02970.1568-0.0601-0.03150.08380.04460.0054-0.09250.0044-0.00880.234-3.553918.60319.2077
31.11460.2720.06640.68120.18450.32250.0048-0.11360.0992-0.0086-0.0247-0.0079-0.0220.00220.01990.0382-0.0091-0.05680.0406-0.00880.103112.99186.584127.2379
41.91090.1990.23650.76810.25570.36250.0276-0.1259-0.26960.0452-0.0009-0.05360.01770.0089-0.02670.0307-0.0023-0.04970.01780.02370.11197.8041-14.591224.7914
51.63940.34890.2340.64810.13230.31170.00360.0748-0.1637-0.02130.00650.01940.00690.0092-0.01010.0273-0.0042-0.04970.0194-0.00390.1088-11.8495-15.796815.142
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 103
2X-RAY DIFFRACTION2B1 - 103
3X-RAY DIFFRACTION3C1 - 103
4X-RAY DIFFRACTION4D1 - 103
5X-RAY DIFFRACTION5E1 - 103

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