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- PDB-8aij: STRUCTURE OF THE LECB LECTIN FROM PSEUDOMONAS AERUGINOSA STRAIN P... -

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Basic information

Entry
Database: PDB / ID: 8aij
TitleSTRUCTURE OF THE LECB LECTIN FROM PSEUDOMONAS AERUGINOSA STRAIN PAO1 IN COMPLEX WITH N-(alpha-L-Fucopyranosyl)benzamide (6)
ComponentsFucose-binding lectin PA-IIL
KeywordsSUGAR BINDING PROTEIN / P. aeruginosa lectin / LecB / Inhibitor
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 / N-(alpha-L-Fucopyranosyl)benzamide / Fucose-binding lectin PA-IIL
Function and homology information
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsMeiers, J. / Mala, P. / Varrot, A. / Siebs, E. / Imberty, A. / Titz, A.
Funding support France, 1items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANR-17-CE11-0048 France
CitationJournal: J.Med.Chem. / Year: 2022
Title: Discovery of N -beta-l-Fucosyl Amides as High-Affinity Ligands for the Pseudomonas aeruginosa Lectin LecB.
Authors: Mala, P. / Siebs, E. / Meiers, J. / Rox, K. / Varrot, A. / Imberty, A. / Titz, A.
History
DepositionJul 26, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 2, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 9, 2022Group: 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
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AAA: Fucose-binding lectin PA-IIL
BBB: Fucose-binding lectin PA-IIL
CCC: Fucose-binding lectin PA-IIL
DDD: Fucose-binding lectin PA-IIL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,57720
Polymers46,9394
Non-polymers1,63816
Water9,170509
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, P. aeruginosa LecB is well described in literature, e.g. by Imberty et al., Gilboa-Carter et al., Titz et al..
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.376, 51.589, 52.604
Angle α, β, γ (deg.)101.809, 99.474, 115.811
Int Tables number1
Space group name H-MP1

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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) / Gene: lecB, PA3361 / 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
#3: Chemical
ChemComp-M9I / N-(alpha-L-Fucopyranosyl)benzamide / ~{N}-[(2~{R},3~{S},4~{R},5~{S},6~{S})-6-methyl-3,4,5-tris(oxidanyl)oxan-2-yl]benzamide


Mass: 267.278 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C13H17NO5 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 509 / Source method: isolated from a natural source / Formula: H2O
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: 2.21 Å3/Da / Density % sol: 44.44 % / Description: plates
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 4.4
Details: 24% PEG 8K, 1M LiCl and 100 mM sodium acetate pH = 4.4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.9801 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jun 19, 2022
Details: Cryogenically cooled channel cut crystal monochromator, a convex prefocussing mirror and a Kirkpatrick-Baez pair of focussing mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9801 Å / Relative weight: 1
ReflectionResolution: 1.5→40.69 Å / Num. obs: 211861 / % possible obs: 95.5 % / Redundancy: 3.4 % / CC1/2: 0.997 / Rmerge(I) obs: 0.051 / Rpim(I) all: 0.051 / Rrim(I) all: 0.072 / Net I/σ(I): 12.9
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 3.3 % / Rmerge(I) obs: 1.53 / Mean I/σ(I) obs: 3.4 / Num. unique obs: 9941 / CC1/2: 0.881 / Rpim(I) all: 0.318 / Rrim(I) all: 0.45 / % possible all: 92.49

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5A3O

5a3o


Resolution: 1.5→40.69 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.966 / SU B: 1.154 / SU ML: 0.043 / Cross valid method: FREE R-VALUE / ESU R: 0.072 / ESU R Free: 0.074
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.1688 7571 12.291 %random selection
Rwork0.1383 54018 --
all0.142 ---
obs-61588 95.507 %-
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: 15.5 Å2
Baniso -1Baniso -2Baniso -3
1-0.341 Å20.222 Å2-0.038 Å2
2--0.097 Å20.067 Å2
3----0.542 Å2
Refinement stepCycle: LAST / Resolution: 1.5→40.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3286 0 100 509 3895
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0133578
X-RAY DIFFRACTIONr_bond_other_d0.0010.0153297
X-RAY DIFFRACTIONr_angle_refined_deg1.8241.6284935
X-RAY DIFFRACTIONr_angle_other_deg1.6091.5737527
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0665491
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.36126.049162
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.67915486
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.432157
X-RAY DIFFRACTIONr_chiral_restr0.0950.2512
X-RAY DIFFRACTIONr_gen_planes_refined0.010.024424
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02854
X-RAY DIFFRACTIONr_nbd_refined0.2520.2645
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2050.22965
X-RAY DIFFRACTIONr_nbtor_refined0.1640.21829
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0870.21932
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1610.2316
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1030.22
X-RAY DIFFRACTIONr_metal_ion_refined0.0680.230
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2190.29
X-RAY DIFFRACTIONr_nbd_other0.2130.262
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1810.232
X-RAY DIFFRACTIONr_mcbond_it1.3191.2521919
X-RAY DIFFRACTIONr_mcbond_other1.3141.2521917
X-RAY DIFFRACTIONr_mcangle_it1.9071.8782425
X-RAY DIFFRACTIONr_mcangle_other1.9071.8782425
X-RAY DIFFRACTIONr_scbond_it2.3341.4961659
X-RAY DIFFRACTIONr_scbond_other2.3341.4971660
X-RAY DIFFRACTIONr_scangle_it3.4132.1532510
X-RAY DIFFRACTIONr_scangle_other3.4122.1542511
X-RAY DIFFRACTIONr_lrange_it4.74717.4793932
X-RAY DIFFRACTIONr_lrange_other4.74817.4623930
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.5390.2475280.2073873X-RAY DIFFRACTION92.3416
1.539-1.5810.225350.1783819X-RAY DIFFRACTION93.715
1.581-1.6270.25040.1653808X-RAY DIFFRACTION94.7692
1.627-1.6770.2125290.1543639X-RAY DIFFRACTION94.9863
1.677-1.7320.194780.1473564X-RAY DIFFRACTION95.2628
1.732-1.7920.1694950.1383401X-RAY DIFFRACTION95.2102
1.792-1.860.1814530.1373342X-RAY DIFFRACTION95.3997
1.86-1.9360.1674820.1313174X-RAY DIFFRACTION95.782
1.936-2.0220.1524180.1253084X-RAY DIFFRACTION95.1889
2.022-2.120.1624310.1242905X-RAY DIFFRACTION95.1783
2.12-2.2350.1553770.1212817X-RAY DIFFRACTION96.2338
2.235-2.370.1683640.1272692X-RAY DIFFRACTION96.5866
2.37-2.5330.1753430.1362497X-RAY DIFFRACTION96.4346
2.533-2.7360.1663110.1382382X-RAY DIFFRACTION97.4665
2.736-2.9960.1643260.1342168X-RAY DIFFRACTION97.6125
2.996-3.3480.1552590.1351942X-RAY DIFFRACTION97.1315
3.348-3.8630.1522560.1311707X-RAY DIFFRACTION96.8426
3.863-4.7240.1522080.1281495X-RAY DIFFRACTION98.7819
4.724-6.650.1531800.1411118X-RAY DIFFRACTION98.1104
6.65-40.690.182930.18591X-RAY DIFFRACTION93.0612

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