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- PDB-5lzi: Porcine heat-labile enterotoxin R13H in complex with inhibitor MM146 -

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Basic information

Entry
Database: PDB / ID: 5lzi
TitlePorcine heat-labile enterotoxin R13H in complex with inhibitor MM146
ComponentsHeat-labile enterotoxin B chain
KeywordsTOXIN / heat-labile enterotoxin / inhibitor / cholera
Function / homology
Function and homology information


toxin activity / killing of cells of another organism / extracellular region
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-7BQ / Chem-7DB / DI(HYDROXYETHYL)ETHER / PHOSPHATE ION / Heat-labile enterotoxin B chain
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsHeggelund, J.E. / Mackenzie, A. / 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 / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.d_res_low
Revision 1.3Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Heat-labile enterotoxin B chain
B: Heat-labile enterotoxin B chain
C: Heat-labile enterotoxin B chain
D: Heat-labile enterotoxin B chain
E: Heat-labile enterotoxin B chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,37817
Polymers58,9425
Non-polymers4,43512
Water14,592810
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14750 Å2
ΔGint-59 kcal/mol
Surface area22400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.170, 75.870, 125.180
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 5 molecules ABCDE

#1: Protein
Heat-labile enterotoxin B chain / LT-B / porcine / LTP-B


Mass: 11788.492 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: eltB, ltpB / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P32890

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Non-polymers , 6 types, 822 molecules

#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-7BQ / (2~{R},4~{S},5~{R},6~{R})-5-acetamido-2-[4-[(2~{R})-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-2-(2-phenylethanoylamino)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: 754.739 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C32H46N6O15
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C4H10O3
#5: Chemical
ChemComp-7DB / (2~{R},4~{S},5~{R},6~{R})-5-acetamido-2-[4-[(2~{S})-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-2-(2-phenylethanoylamino)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: 754.739 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C32H46N6O15
#6: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 810 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.54 Å3/Da / Density % sol: 51.66 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: Sodium cacodylate, PEG

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.9334 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 26, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9334 Å / Relative weight: 1
ReflectionResolution: 1.6→29.2 Å / Num. obs: 74271 / % possible obs: 92.9 % / Redundancy: 2.9 % / CC1/2: 0.996 / Rmerge(I) obs: 0.055 / Net I/σ(I): 10.9
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 2 % / Rmerge(I) obs: 0.219 / Mean I/σ(I) obs: 3.1 / CC1/2: 0.902 / % possible all: 61.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
REFMAC5.8.0155refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1EFI

1efi


Resolution: 1.6→29.2 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.956 / Occupancy max: 1 / Occupancy min: 0.3 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.082 / ESU R Free: 0.082 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1758 3766 5.1 %RANDOM
Rwork0.147 70449 --
obs0.1485 74215 92.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 67.76 Å2 / Biso mean: 17.9038 Å2 / Biso min: 5.78 Å2
Baniso -1Baniso -2Baniso -3
1-0.26 Å20 Å20 Å2
2--0.19 Å20 Å2
3----0.46 Å2
Refinement stepCycle: LAST / Resolution: 1.6→29.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4115 0 307 810 5232
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.024736
X-RAY DIFFRACTIONr_bond_other_d00.024509
X-RAY DIFFRACTIONr_angle_refined_deg2.2362.0376436
X-RAY DIFFRACTIONr_angle_other_deg3.5893.02310512
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0845552
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.53325.879182
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.46715881
X-RAY DIFFRACTIONr_dihedral_angle_4_deg29.2531515
X-RAY DIFFRACTIONr_chiral_restr0.1290.2769
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0215067
X-RAY DIFFRACTIONr_gen_planes_other0.0250.02956
X-RAY DIFFRACTIONr_mcbond_it1.1271.0342166
X-RAY DIFFRACTIONr_mcbond_other1.1261.0342166
X-RAY DIFFRACTIONr_mcangle_it1.6311.5382720
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.263 186 -
Rwork0.216 3482 -
all-3668 -
obs--62.66 %
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)
11.29480.4042-0.24960.8112-0.34430.95710.0081-0.0505-0.01150.04590.0112-0.1145-0.01570.1137-0.01930.00280.0018-0.00730.0193-0.01310.023297.25183.63935.386
20.9650.25050.18140.64140.19611.8787-0.04440.1334-0.0318-0.1270.0554-0.0543-0.06120.1515-0.01090.0281-0.01620.01570.0362-0.00950.026199.19582.39813.491
31.50610.16170.37970.47540.12041.41370.03210.0471-0.0283-0.023-0.00920.0339-0.0417-0.0375-0.0230.02890.00540.0030.0134-0.00220.005179.84575.8525.362
41.1909-0.1081-0.6380.65970.40411.638-0.0069-0.0126-0.07120.0329-0.02470.06410.0761-0.16660.03160.0091-0.0128-0.00580.0419-0.0010.029165.85173.18422.145
51.14820.27860.16620.56390.3781.6638-0.018-0.0685-0.0240.0706-0.00340.0050.0506-0.03420.02130.01370.00750.00510.01470.00780.005476.6277840.77
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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