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- PDB-9g3r: LecA from Pseudomonas aeruginosa in complex with a synthetic thio... -

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Basic information

Entry
Database: PDB / ID: 9g3r
TitleLecA from Pseudomonas aeruginosa in complex with a synthetic thiogalactoside
ComponentsPA-I galactophilic lectin
KeywordsSUGAR BINDING PROTEIN / lectin / cell adhesion / LecA / PA-IL / galactose-binding
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
DI(HYDROXYETHYL)ETHER / 1-thio-beta-D-galactopyranose / PA-I galactophilic lectin
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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: PA-I galactophilic lectin
B: PA-I galactophilic lectin
C: PA-I galactophilic lectin
D: PA-I galactophilic lectin
E: PA-I galactophilic lectin
F: PA-I galactophilic lectin
G: PA-I galactophilic lectin
H: PA-I galactophilic lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,03027
Polymers102,1618
Non-polymers2,86919
Water6,359353
1
A: PA-I galactophilic lectin
F: PA-I galactophilic lectin
G: PA-I galactophilic lectin
hetero molecules

D: PA-I galactophilic lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,50013
Polymers51,0814
Non-polymers1,4199
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_655x+1,y,z1
2
B: PA-I galactophilic lectin
C: PA-I galactophilic lectin
H: PA-I galactophilic lectin
hetero molecules

E: PA-I galactophilic lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,53014
Polymers51,0814
Non-polymers1,45010
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_455x-1,y,z1
Unit cell
Length a, b, c (Å)50.900, 99.823, 86.838
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 8 molecules ABCDEFGH

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


Mass: 12770.137 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: ATCC 15692 / Gene: lecA, pa1L, PA2570 / Production host: Escherichia coli (E. coli) / References: UniProt: Q05097

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Sugars , 2 types, 8 molecules

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


Type: oligosaccharide / Mass: 342.362 Da / Num. of mol.: 5 / 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
#5: Sugar ChemComp-YIO / 1-thio-beta-D-galactopyranose / (2R,3R,4S,5R,6S)-2-(HYDROXYMETHYL)-6-SULFANYL-OXANE-3,4,5-TRIOL / 1-thio-beta-D-galactose / 1-thio-D-galactose / 1-thio-galactose


Type: D-saccharide, beta linking / Mass: 196.221 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H12O5S
IdentifierTypeProgram
b-D-Galp1SHIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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Non-polymers , 4 types, 364 molecules

#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#7: 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
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: 2.16 Å3/Da / Density % sol: 43.04 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / Details: PEG 8000, PEG 1000, magnesium chloride, Tris

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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 EIGER2 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: 1.7→49.91 Å / Num. obs: 93512 / % possible obs: 98.3 % / Redundancy: 6.7 % / CC1/2: 0.992 / Rmerge(I) obs: 0.136 / Rpim(I) all: 0.057 / Rrim(I) all: 0.147 / Net I/σ(I): 8.5
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 7 % / Rmerge(I) obs: 0.695 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 13554 / CC1/2: 0.834 / Rpim(I) all: 0.281 / Rrim(I) all: 0.751 / % possible all: 98.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
autoPROCdata reduction
SCALAdata scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→45.386 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.932 / SU B: 2.48 / SU ML: 0.082 / Cross valid method: FREE R-VALUE / ESU R: 0.125 / ESU R Free: 0.117
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2269 4735 5.065 %
Rwork0.196 88746 -
all0.198 --
obs-93481 98.177 %
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: 19.113 Å2
Baniso -1Baniso -2Baniso -3
1-0.271 Å20 Å2-0.174 Å2
2--1.105 Å20 Å2
3----1.375 Å2
Refinement stepCycle: LAST / Resolution: 1.7→45.386 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7153 0 169 353 7675
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0127602
X-RAY DIFFRACTIONr_bond_other_d0.0010.0166899
X-RAY DIFFRACTIONr_angle_refined_deg1.5641.75710430
X-RAY DIFFRACTIONr_angle_other_deg0.5491.72515873
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7995996
X-RAY DIFFRACTIONr_dihedral_angle_2_deg6.526516
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.176101030
X-RAY DIFFRACTIONr_dihedral_angle_6_deg13.49510320
X-RAY DIFFRACTIONr_chiral_restr0.0790.21174
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.029206
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021738
X-RAY DIFFRACTIONr_nbd_refined0.2010.21084
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1880.25660
X-RAY DIFFRACTIONr_nbtor_refined0.1690.23706
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0830.23660
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0990.2266
X-RAY DIFFRACTIONr_metal_ion_refined0.0890.223
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1270.231
X-RAY DIFFRACTIONr_nbd_other0.280.2120
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.0970.214
X-RAY DIFFRACTIONr_mcbond_it1.6581.8963900
X-RAY DIFFRACTIONr_mcbond_other1.6581.8963900
X-RAY DIFFRACTIONr_mcangle_it2.4123.4094870
X-RAY DIFFRACTIONr_mcangle_other2.4123.414871
X-RAY DIFFRACTIONr_scbond_it2.172.1543702
X-RAY DIFFRACTIONr_scbond_other2.1692.1543703
X-RAY DIFFRACTIONr_scangle_it3.3423.8575542
X-RAY DIFFRACTIONr_scangle_other3.3413.8575543
X-RAY DIFFRACTIONr_lrange_it4.22620.127888
X-RAY DIFFRACTIONr_lrange_other4.22620.1217889
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.7-1.7440.3023710.24364830.24769870.9510.96598.09650.227
1.744-1.7920.2463230.22263640.22368030.960.9798.29490.204
1.792-1.8440.263100.21162720.21366760.9570.97398.5920.193
1.844-1.90.2733490.20259930.20664680.9530.97598.05190.187
1.9-1.9630.2582790.19259350.19562910.9590.97798.7760.177
1.963-2.0310.213160.19354790.19460250.9730.97796.18260.183
2.031-2.1080.2292740.19554210.19758570.9670.97797.23410.186
2.108-2.1940.2393030.19652710.19856340.9670.97798.9350.189
2.194-2.2910.2432320.19251320.19554190.9640.97898.98510.186
2.291-2.4030.2382590.18748740.1951750.9670.97999.18840.183
2.403-2.5320.2392100.18946350.19248940.9620.97898.99880.188
2.532-2.6850.2092430.18743500.18846510.9720.97898.7530.189
2.685-2.870.2532270.20240280.20443740.960.97497.27940.206
2.87-3.0990.2422390.21736860.21940690.9620.9796.4610.223
3.099-3.3930.2112020.21135550.21137770.9710.97499.47050.224
3.393-3.7910.2071550.231850.233750.9760.97898.9630.212
3.791-4.3720.1811480.16628440.16730230.980.98598.97450.189
4.372-5.3420.1871270.16523800.16625590.9870.98797.9680.19
5.342-7.5030.2341040.19917970.20120040.9790.98494.86030.228
7.503-45.3860.244640.21310620.21511520.9710.97497.74310.239

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