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- PDB-9g3k: LecB from PA01 in complex with synthetic beta - fucosylamide -

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Basic information

Entry
Database: PDB / ID: 9g3k
TitleLecB from PA01 in complex with synthetic beta - fucosylamide
ComponentsFucose-binding lectin PA-IIL
KeywordsSUGAR BINDING PROTEIN / Lectin / beta-fucosylamide / anti-adhesive / Pseudomonas
Function / homologyLectin, sugar-binding / Calcium-mediated lectin / Calcium-mediated lectin superfamily / Fucose-binding lectin II (PA-IIL) / single-species biofilm formation / carbohydrate binding / metal ion binding / Chem-R7E / Fucose-binding lectin PA-IIL
Function and homology information
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsAntonini, G. / Varrot, A.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Union (EU)765581European Union
CitationJournal: J.Med.Chem. / Year: 2025
Title: Toward Dual-Target Glycomimetics against Two Bacterial Lectins to Fight Pseudomonas aeruginosa - Burkholderia cenocepacia Infections: A Biophysical Study.
Authors: Antonini, G. / Fares, M. / Hauck, D. / Mala, P. / Gillon, E. / Belvisi, L. / Bernardi, A. / Titz, A. / Varrot, A. / Mazzotta, S.
History
DepositionJul 12, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 16, 2025Provider: repository / Type: Initial release
Revision 1.1May 7, 2025Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2May 21, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fucose-binding lectin PA-IIL
B: Fucose-binding lectin PA-IIL
C: Fucose-binding lectin PA-IIL
D: Fucose-binding lectin PA-IIL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,10218
Polymers46,9394
Non-polymers1,16314
Water10,395577
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9490 Å2
ΔGint-195 kcal/mol
Surface area15930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.351, 80.166, 52.406
Angle α, β, γ (deg.)90.000, 109.361, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Fucose-binding lectin PA-IIL


Mass: 11734.707 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Strain: PAO1 / Gene: lecB, PA3361 / Plasmid: PET25B-LecB / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9HYN5
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-R7E / 5-[3-(aminomethyl)phenyl]-~{N}-[(2~{S},3~{S},4~{R},5~{S},6~{S})-6-methyl-3,4,5-tris(oxidanyl)oxan-2-yl]furan-2-carboxamide / (5-(3'-aminomethyl)phenyl)furan-2-carboxamido-b-L-fucopyranose


Mass: 362.377 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H22N2O6 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 577 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 4.22 Å3/Da / Density % sol: 70.86 % / Description: rod
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / Details: 30% PEG 5KMME 0.2M AmSO4 0.1M Mes pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.98011 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Nov 17, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98011 Å / Relative weight: 1
ReflectionResolution: 1.55→47.5 Å / Num. obs: 268205 / % possible obs: 99.7 % / Redundancy: 4.7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.048 / Rpim(I) all: 0.036 / Rrim(I) all: 0.06 / Net I/σ(I): 15.5
Reflection shellResolution: 1.55→1.58 Å / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 3.5 / Num. unique obs: 12508 / CC1/2: 0.922 / Rpim(I) all: 0.289 / Rrim(I) all: 0.471

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.55→47.5 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.963 / SU B: 1.283 / SU ML: 0.046 / Cross valid method: FREE R-VALUE / ESU R: 0.07 / ESU R Free: 0.073
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1682 2853 5.026 %
Rwork0.1366 53908 -
all0.138 --
obs-56761 99.661 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 14.11 Å2
Baniso -1Baniso -2Baniso -3
1--0.436 Å2-0 Å2-0.353 Å2
2--1.217 Å20 Å2
3----0.427 Å2
Refinement stepCycle: LAST / Resolution: 1.55→47.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3295 0 59 577 3931
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0113486
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163196
X-RAY DIFFRACTIONr_angle_refined_deg1.8341.744807
X-RAY DIFFRACTIONr_angle_other_deg0.6791.7047289
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6555476
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.846511
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.76910480
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.86610154
X-RAY DIFFRACTIONr_chiral_restr0.1060.2599
X-RAY DIFFRACTIONr_gen_planes_refined0.010.024340
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02821
X-RAY DIFFRACTIONr_nbd_refined0.230.2582
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2180.22822
X-RAY DIFFRACTIONr_nbtor_refined0.1720.21773
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0920.22017
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1510.2384
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0350.22
X-RAY DIFFRACTIONr_metal_ion_refined0.0690.226
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.0710.29
X-RAY DIFFRACTIONr_nbd_other0.1840.257
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1520.243
X-RAY DIFFRACTIONr_mcbond_it1.651.3681880
X-RAY DIFFRACTIONr_mcbond_other1.6411.3671879
X-RAY DIFFRACTIONr_mcangle_it2.3252.4472364
X-RAY DIFFRACTIONr_mcangle_other2.3252.4472365
X-RAY DIFFRACTIONr_scbond_it3.1621.6581606
X-RAY DIFFRACTIONr_scbond_other3.1081.6411587
X-RAY DIFFRACTIONr_scangle_it4.5372.9162443
X-RAY DIFFRACTIONr_scangle_other4.5112.8812414
X-RAY DIFFRACTIONr_lrange_it5.71519.423909
X-RAY DIFFRACTIONr_lrange_other5.38815.2133726
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.55-1.590.2642120.2513996X-RAY DIFFRACTION99.6448
1.634-1.6810.1961920.183787X-RAY DIFFRACTION99.9749
1.681-1.7330.1872040.1593642X-RAY DIFFRACTION99.948
1.733-1.7890.2021790.1433545X-RAY DIFFRACTION99.9463
1.789-1.8520.1811730.1353452X-RAY DIFFRACTION99.9173
1.852-1.9220.1692090.1293288X-RAY DIFFRACTION99.7718
1.922-20.161690.1283192X-RAY DIFFRACTION99.6442
2-2.0890.1721750.1333034X-RAY DIFFRACTION99.6584
2.089-2.1910.1661760.1332914X-RAY DIFFRACTION99.5169
2.191-2.3090.1471450.1262761X-RAY DIFFRACTION99.5546
2.309-2.4490.1761400.1192614X-RAY DIFFRACTION99.2432
2.449-2.6170.1361090.112508X-RAY DIFFRACTION98.9788
2.617-2.8260.1451420.1242273X-RAY DIFFRACTION99.711
2.826-3.0950.1541000.1282137X-RAY DIFFRACTION99.4222
3.095-3.4590.1441030.1261929X-RAY DIFFRACTION99.559
3.459-3.990.156830.1171719X-RAY DIFFRACTION99.503
3.99-4.8780.185560.1131459X-RAY DIFFRACTION99.4747
4.878-6.8630.207480.1731140X-RAY DIFFRACTION99.6644
6.863-47.50.155350.193645X-RAY DIFFRACTION98.6938

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