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- PDB-9g3s: LecB from Pseudomonas aeruginosa in complex with a synthetic thio... -

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Basic information

Entry
Database: PDB / ID: 9g3s
TitleLecB from Pseudomonas aeruginosa in complex with a synthetic thiofucoside
ComponentsFucose-binding lectin PA-IIL
KeywordsSUGAR BINDING PROTEIN / lectin / cell adhesion / LecA / PA-IIL / fucose-binding
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 / Fucose-binding lectin PA-IIL
Function and homology information
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsMelicher, F. / Faltinek, L. / Wimmerova, M.
Funding support Czech Republic, 1items
OrganizationGrant numberCountry
Ministry of Education, Youth and Sports of the Czech RepublicLM2023042 Czech Republic
CitationJournal: Chemistry / Year: 2025
Title: Bispecific Thio-Linked Disaccharides as Inhibitors of Pseudomonas Aeruginosa Lectins LecA (PA-IL) and LecB (PA-IIL): Dual-Targeting Strategy.
Authors: Faltinek, L. / Melicher, F. / Kelemen, V. / Mezo, E. / Borbas, A. / Wimmerova, M.
History
DepositionJul 12, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 27, 2024Provider: repository / Type: Initial release
Revision 1.1Feb 5, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.title ..._citation.journal_volume / _citation.title / _citation.year / _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
E: Fucose-binding lectin PA-IIL
F: Fucose-binding lectin PA-IIL
G: Fucose-binding lectin PA-IIL
H: Fucose-binding lectin PA-IIL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,56356
Polymers93,8788
Non-polymers5,68648
Water3,459192
1
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)49,68627
Polymers46,9394
Non-polymers2,74723
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10120 Å2
ΔGint-240 kcal/mol
Surface area16350 Å2
MethodPISA
2
E: Fucose-binding lectin PA-IIL
F: Fucose-binding lectin PA-IIL
G: Fucose-binding lectin PA-IIL
H: Fucose-binding lectin PA-IIL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,87829
Polymers46,9394
Non-polymers2,93925
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10450 Å2
ΔGint-259 kcal/mol
Surface area16930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.488, 96.951, 128.680
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, 8 molecules ABCDEFGH

#1: Protein
Fucose-binding lectin PA-IIL


Mass: 11734.707 Da / Num. of mol.: 8
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

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Sugars , 2 types, 8 molecules

#2: Polysaccharide
alpha-L-fucopyranose-(1-1)-1-thio-beta-D-galactopyranose


Type: oligosaccharide / Mass: 342.362 Da / Num. of mol.: 7 / Source method: obtained synthetically
DescriptorTypeProgram
WURCS=2.0/2,2,1/[a2112h-1b_1-5][a1221m-1a_1-5]/1-2/a1-b1*S*WURCSPDB2Glycan 1.1.0
[][a-L-Fucp1SH]{[(1+S)][b-D-Galp]{}}LINUCSPDB-CARE
#3: Polysaccharide 1-thio-beta-D-galactopyranose-(1-1)-alpha-L-fucopyranose


Type: oligosaccharide / Mass: 342.362 Da / Num. of mol.: 1 / Source method: obtained synthetically
DescriptorTypeProgram
WURCS=2.0/2,2,1/[a2112h-1b_1-5][a1221m-1a_1-5]/1-2/a1-b1*S*WURCSPDB2Glycan 1.1.0
[][a-L-Fucp]{[(1+S)][b-D-Galp1SH]{}}LINUCSPDB-CARE

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Non-polymers , 3 types, 232 molecules

#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Ca
#5: Chemical...
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 192 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.47 Å3/Da / Density % sol: 50.3 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: PEG 8000, Tris, ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.976 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 19, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.85→48.69 Å / Num. obs: 80145 / % possible obs: 99.9 % / Redundancy: 13.6 % / CC1/2: 0.999 / Net I/σ(I): 12
Reflection shellResolution: 1.85→1.95 Å / Mean I/σ(I) obs: 2.2 / Num. unique obs: 11547 / CC1/2: 0.753

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
autoPROCdata reduction
SCALAdata scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.85→48.69 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.955 / SU B: 3.23 / SU ML: 0.095 / Cross valid method: FREE R-VALUE / ESU R: 0.136 / ESU R Free: 0.127
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2194 3930 4.909 %
Rwork0.1854 76134 -
all0.187 --
obs-80064 99.87 %
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: 24.788 Å2
Baniso -1Baniso -2Baniso -3
1--0.89 Å2-0 Å20 Å2
2---0.558 Å2-0 Å2
3---1.447 Å2
Refinement stepCycle: LAST / Resolution: 1.85→48.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6596 0 312 192 7100
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0127046
X-RAY DIFFRACTIONr_bond_other_d0.0010.0166407
X-RAY DIFFRACTIONr_angle_refined_deg1.4771.7549699
X-RAY DIFFRACTIONr_angle_other_deg0.5411.70114627
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2225930
X-RAY DIFFRACTIONr_dihedral_angle_2_deg6.037514
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.58710948
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.18810301
X-RAY DIFFRACTIONr_chiral_restr0.0720.21261
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.028402
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021582
X-RAY DIFFRACTIONr_nbd_refined0.2270.21165
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2020.25590
X-RAY DIFFRACTIONr_nbtor_refined0.1640.23621
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0880.23890
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1450.2302
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1650.24
X-RAY DIFFRACTIONr_metal_ion_refined0.0820.256
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2120.216
X-RAY DIFFRACTIONr_nbd_other0.1540.250
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1180.212
X-RAY DIFFRACTIONr_mcbond_it1.8492.4263693
X-RAY DIFFRACTIONr_mcbond_other1.8492.4263692
X-RAY DIFFRACTIONr_mcangle_it2.4734.3414620
X-RAY DIFFRACTIONr_mcangle_other2.4724.3414621
X-RAY DIFFRACTIONr_scbond_it2.8282.743353
X-RAY DIFFRACTIONr_scbond_other2.8282.743354
X-RAY DIFFRACTIONr_scangle_it4.2514.9145075
X-RAY DIFFRACTIONr_scangle_other4.2514.9135076
X-RAY DIFFRACTIONr_lrange_it4.91225.5317265
X-RAY DIFFRACTIONr_lrange_other4.91225.5317266
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.8980.3292740.2815564X-RAY DIFFRACTION99.7267
1.898-1.950.2552730.2395421X-RAY DIFFRACTION99.9473
1.95-2.0060.2462590.2145291X-RAY DIFFRACTION99.91
2.006-2.0680.2492450.2025171X-RAY DIFFRACTION99.9262
2.068-2.1360.252670.1914941X-RAY DIFFRACTION99.9808
2.136-2.210.2232530.184803X-RAY DIFFRACTION99.9012
2.21-2.2940.242260.1784648X-RAY DIFFRACTION99.8566
2.294-2.3870.2422460.174490X-RAY DIFFRACTION99.9789
2.387-2.4930.2412250.1744311X-RAY DIFFRACTION100
2.493-2.6140.222080.1834134X-RAY DIFFRACTION100
2.614-2.7550.2312340.1813895X-RAY DIFFRACTION100
2.755-2.9220.2391980.1913718X-RAY DIFFRACTION99.949
2.922-3.1230.2291940.1953504X-RAY DIFFRACTION99.9459
3.123-3.3720.2241710.1893263X-RAY DIFFRACTION99.4498
3.372-3.6920.2051550.1613023X-RAY DIFFRACTION99.8743
3.692-4.1250.1751370.1692776X-RAY DIFFRACTION100
4.125-4.7570.1761540.1612411X-RAY DIFFRACTION99.9221
4.757-5.8130.156940.1622115X-RAY DIFFRACTION99.9548
5.813-8.1630.247750.2041656X-RAY DIFFRACTION98.6325
8.163-48.690.179420.206999X-RAY DIFFRACTION99.8082

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