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- PDB-7z62: Structure of the LecA lectin from Pseudomonas aeruginosa in compl... -

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Basic information

Entry
Database: PDB / ID: 7z62
TitleStructure of the LecA lectin from Pseudomonas aeruginosa in complex with a biaryl-thiogalactoside
ComponentsPA-I galactophilic lectin
KeywordsSUGAR BINDING PROTEIN / lectin / antiadhesive / thiogalactoside / RNA BINDING PROTEIN
Function / homology
Function and homology information


heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / 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
Chem-IEC / PA-I galactophilic lectin
Similarity search - Component
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.53 Å
AuthorsVarrot, A.
Funding support France, 1items
OrganizationGrant numberCountry
Centre National de la Recherche Scientifique (CNRS) France
CitationJournal: Eur.J.Med.Chem. / Year: 2022
Title: Discovery of potent 1,1-diarylthiogalactoside glycomimetic inhibitors of Pseudomonas aeruginosa LecA with antibiofilm properties.
Authors: Bruneau, A. / Gillon, E. / Furiga, A. / Brachet, E. / Alami, M. / Roques, C. / Varrot, A. / Imberty, A. / Messaoudi, S.
History
DepositionMar 10, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 18, 2023Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AAA: PA-I galactophilic lectin
BBB: PA-I galactophilic lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,1497
Polymers25,5402
Non-polymers6095
Water7,026390
1
AAA: PA-I galactophilic lectin
BBB: PA-I galactophilic lectin
hetero molecules

AAA: PA-I galactophilic lectin
BBB: PA-I galactophilic lectin
hetero molecules


  • defined by author
  • Evidence: gel filtration
  • 52.3 kDa, 4 polymers
Theoretical massNumber of molelcules
Total (without water)52,29814
Polymers51,0814
Non-polymers1,21810
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
Unit cell
Length a, b, c (Å)48.122, 57.089, 83.399
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11AAA-491-

HOH

21BBB-470-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11AAA
21BBB

NCS domain segments:

Ens-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: SER / End label comp-ID: SER / Auth seq-ID: 1 - 121 / Label seq-ID: 1 - 121

Dom-IDComponent-IDAuth asym-IDLabel asym-ID
11AAAA
22BBBB

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

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Components

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


Mass: 12770.137 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: N TERMINAL METHIONINE PROCESSED / Source: (gene. exp.) Pseudomonas aeruginosa 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
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-IEC / (2R,3R,4S,5R,6S)-2-(hydroxymethyl)-6-[4-[1-(4-methoxyphenyl)ethenyl]phenyl]sulfanyl-oxane-3,4,5-triol / Biaryl-thiogalactoside


Mass: 404.477 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H24O6S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 390 / 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: 2.25 Å3/Da / Density % sol: 45.4 % / Description: rod
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 18% PEG3350, 150 mM KSCN, 100 mM Tris/HCl pH 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 13, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.53→41.7 Å / Num. obs: 35361 / % possible obs: 99.8 % / Redundancy: 9.2 % / Biso Wilson estimate: 13.4 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.0042 / Rpim(I) all: 0.0021 / Rrim(I) all: 0.0047 / Net I/σ(I): 26.5
Reflection shellResolution: 1.53→1.56 Å / Redundancy: 9.3 % / Rmerge(I) obs: 0.264 / Mean I/σ(I) obs: 7.3 / Num. unique obs: 1733 / CC1/2: 0.987 / Rpim(I) all: 0.134 / Rrim(I) all: 0.297 / % possible all: 99.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
Aimless0.7.3data scaling
PHASER2.8.2phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1OKO

1oko


Resolution: 1.53→41.7 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.954 / WRfactor Rfree: 0.213 / WRfactor Rwork: 0.171 / SU B: 1.318 / SU ML: 0.05 / Average fsc free: 0.9471 / Average fsc work: 0.9561 / Cross valid method: FREE R-VALUE / ESU R: 0.079 / ESU R Free: 0.084
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2061 1749 4.951 %
Rwork0.1656 33577 -
all0.168 --
obs-35326 99.718 %
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: 18.715 Å2
Baniso -1Baniso -2Baniso -3
1-1.294 Å20 Å20 Å2
2--0.739 Å2-0 Å2
3----2.033 Å2
Refinement stepCycle: LAST / Resolution: 1.53→41.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1797 0 38 390 2225
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0131945
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161754
X-RAY DIFFRACTIONr_angle_refined_deg1.891.6512671
X-RAY DIFFRACTIONr_angle_other_deg1.5721.5944029
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4385256
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.78125.22788
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.93515264
X-RAY DIFFRACTIONr_dihedral_angle_4_deg5.663154
X-RAY DIFFRACTIONr_chiral_restr0.0960.2256
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.022360
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02462
X-RAY DIFFRACTIONr_nbd_refined0.2270.2338
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1940.21609
X-RAY DIFFRACTIONr_nbtor_refined0.1760.2972
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0840.2940
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1470.2254
X-RAY DIFFRACTIONr_metal_ion_refined0.0930.25
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1460.211
X-RAY DIFFRACTIONr_nbd_other0.2030.287
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.160.243
X-RAY DIFFRACTIONr_mcbond_it1.6931.7491006
X-RAY DIFFRACTIONr_mcbond_other1.6771.7481005
X-RAY DIFFRACTIONr_mcangle_it2.272.6221268
X-RAY DIFFRACTIONr_mcangle_other2.2712.6231269
X-RAY DIFFRACTIONr_scbond_it2.4091.958939
X-RAY DIFFRACTIONr_scbond_other2.4081.959940
X-RAY DIFFRACTIONr_scangle_it3.4172.8691403
X-RAY DIFFRACTIONr_scangle_other3.4162.8691404
X-RAY DIFFRACTIONr_lrange_it4.74823.052311
X-RAY DIFFRACTIONr_lrange_other4.53821.8692199
X-RAY DIFFRACTIONr_ncsr_local_group_10.1090.053792
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AAAX-RAY DIFFRACTIONLocal ncs0.109370.05009
12BBBX-RAY DIFFRACTIONLocal ncs0.109370.05009
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
1.53-1.570.2491310.20924060.21125550.9250.93599.29550.194
1.57-1.6130.2781240.21323840.21725250.920.93599.32670.196
1.613-1.6590.2251310.18523350.18724720.9470.95299.75730.171
1.659-1.710.2151180.17822060.1823370.9490.95499.44370.164
1.71-1.7660.2071030.17422060.17623150.9490.95799.74080.165
1.766-1.8280.2071000.16621240.16722300.9520.9699.73090.157
1.828-1.8970.21220.1720440.17221690.9460.95599.86170.164
1.897-1.9740.212860.16719860.16920730.9380.95599.95180.163
1.974-2.0620.2061060.17618930.17720010.9520.95599.90.173
2.062-2.1620.23850.17618300.17819150.9460.9581000.174
2.162-2.2790.2191060.16417370.16718430.9430.9591000.166
2.279-2.4170.211830.16216370.16517200.9430.9571000.165
2.417-2.5830.187760.1515580.15216340.9560.9631000.153
2.583-2.7890.174500.15414740.15415240.960.9641000.16
2.789-3.0540.21730.15313340.15614080.9530.96799.9290.163
3.054-3.4120.172750.14412240.14612990.970.9721000.159
3.412-3.9360.228580.1510850.15311460.9510.97199.73820.169
3.936-4.8090.163430.1479480.1489920.9790.97999.89920.17
4.809-6.7570.215520.1867300.1877850.9710.97699.61780.205
6.757-41.70.221270.2414360.2394810.9540.94796.25780.322

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