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- PDB-6yo3: LecA from Pseudomonas aeruginosa in complex with a catechol CAS n... -

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Basic information

Entry
Database: PDB / ID: 6yo3
TitleLecA from Pseudomonas aeruginosa in complex with a catechol CAS no. 67984-81-0
ComponentsPA-I galactophilic lectin
KeywordsSUGAR BINDING PROTEIN / Non-carbohydrate glycomimetics / PAINS / lectin / catechols
Function / homology
Function and homology information


heterophilic cell-cell adhesion / carbohydrate binding / periplasmic space / cell surface / cytoplasm
Similarity search - Function
PA-IL-like / PA-IL-like protein / Galactose-binding-like domain superfamily
Similarity search - Domain/homology
2,3-bis(oxidanyl)benzenecarbonitrile / TRIETHYLENE GLYCOL / PA-I galactophilic lectin
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.84 Å
AuthorsKuhaudomlarp, S. / Imberty, A. / Titz, A.
Funding support France, Germany, 6items
OrganizationGrant numberCountry
French National Research AgencyANR-AAPG-2017 France
French National Research AgencyANR-17-CE11-0048 France
German Research Foundation (DFG)Ti756/5-1 Germany
German Research Foundation (DFG)RA1944/7-1 Germany
French National Research AgencyANR-17-EURE-0003 France
French National Research AgencyANR-15-IDEX02 France
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2021
Title: Non-Carbohydrate Glycomimetics as Inhibitors of Calcium(II)-Binding Lectins.
Authors: Kuhaudomlarp, S. / Siebs, E. / Shanina, E. / Topin, J. / Joachim, I. / da Silva Figueiredo Celestino Gomes, P. / Varrot, A. / Rognan, D. / Rademacher, C. / Imberty, A. / Titz, A.
History
DepositionApr 14, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 30, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 7, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year
Revision 1.2Jan 24, 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: PA-I galactophilic lectin
B: PA-I galactophilic lectin
C: PA-I galactophilic lectin
D: PA-I galactophilic lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,26215
Polymers51,0814
Non-polymers1,18111
Water6,359353
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7470 Å2
ΔGint-17 kcal/mol
Surface area19610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.943, 48.630, 128.632
Angle α, β, γ (deg.)90.000, 95.590, 90.000
Int Tables number5
Space group name H-MI121

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
PA-I galactophilic lectin / PA-IL / Galactose-binding lectin


Mass: 12770.137 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: LecA from Pseudomonas aeruginosa was produced as a recombinant protein in E. coli
Source: (gene. exp.) Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (bacteria)
Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1
Gene: lecA, pa1L, PA2570 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q05097

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Non-polymers , 7 types, 364 molecules

#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-P3K / 2,3-bis(oxidanyl)benzenecarbonitrile


Mass: 135.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H5NO2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 282.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#7: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 353 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.71 Å3/Da / Density % sol: 54.61 %
Crystal growTemperature: 292.15 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 20% PEG6000, 100 mM sodium acetate pH 4.5, 1 M LiCl, 1% DMSO mixed in 1:1 ratio with 10mg/ml of LecA in water containing 100 uM CaCl2. The mixture was deposited onto dried catechol compound ...Details: 20% PEG6000, 100 mM sodium acetate pH 4.5, 1 M LiCl, 1% DMSO mixed in 1:1 ratio with 10mg/ml of LecA in water containing 100 uM CaCl2. The mixture was deposited onto dried catechol compound for co-crystallisation

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9786 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 25, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 1.84→45.5 Å / Num. obs: 47830 / % possible obs: 99.6 % / Redundancy: 5.6 % / CC1/2: 0.997 / Rmerge(I) obs: 0.09 / Rpim(I) all: 0.041 / Rrim(I) all: 0.099 / Net I/σ(I): 11.1
Reflection shell

Diffraction-ID: 1 / Redundancy: 5.4 %

Resolution (Å)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.84-1.880.521583529070.9190.240.5752.797.2
9-45.460.04823744400.9980.0220.05325.397.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
Aimless0.7.4data scaling
PDB_EXTRACT3.25data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1OKO

1oko


Resolution: 1.84→45.46 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.94 / SU B: 2.711 / SU ML: 0.08 / SU R Cruickshank DPI: 0.1208 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.121 / ESU R Free: 0.117
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2077 2432 5.1 %RANDOM
Rwork0.1723 ---
obs0.1741 45394 99.44 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 65.6 Å2 / Biso mean: 21.456 Å2 / Biso min: 8.5 Å2
Baniso -1Baniso -2Baniso -3
1-0.29 Å20 Å21.52 Å2
2--0.77 Å20 Å2
3----1.34 Å2
Refinement stepCycle: final / Resolution: 1.84→45.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3597 0 74 363 4034
Biso mean--32.2 29.82 -
Num. residues----484
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0133799
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173313
X-RAY DIFFRACTIONr_angle_refined_deg1.5651.6365186
X-RAY DIFFRACTIONr_angle_other_deg1.431.5827726
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0215492
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.51725.088171
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.17315517
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.296158
X-RAY DIFFRACTIONr_chiral_restr0.0620.2492
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.024402
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02746
LS refinement shellResolution: 1.84→1.885 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.276 163 -
Rwork0.246 3307 -
obs--97.66 %

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