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- PDB-6yoh: LecA from Pseudomonas aeruginosa in complex with a catechol CAS n... -

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Basic information

Entry
Database: PDB / ID: 6yoh
TitleLecA from Pseudomonas aeruginosa in complex with a catechol CAS no. 61445-50-9
ComponentsPA-I galactophilic lectin
KeywordsSUGAR BINDING PROTEIN / Non-carbohydrate glycomimetics / PAINS / lectin / catechols
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-P4H / PA-I galactophilic lectin
Similarity search - Component
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.84 Å
AuthorsKuhaudomlarp, S. / Imberty, A. / Titz, A. / Varrot, A.
Funding support France, Germany, 6items
OrganizationGrant numberCountry
French National Research AgencyANR-AAPG-2017 France
French National Research AgencyANR-17-CE11-0048 France
German Research Foundation (DFG)Ti756/5-1 Germany
German Research Foundation (DFG)RA1944/7-1 Germany
French National Research AgencyANR-17-EURE-0003 France
French National Research AgencyANR-15-IDEX02 France
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2020
Title: Non-Carbohydrate Glycomimetics as Inhibitors of Calcium(II)-binding Lectins.
Authors: Kuhaudomlarp, S. / Siebs, E. / Shanina, E. / Topin, J. / Joachim, I. / da Silva Figueiredo Celestino Gomes, P. / Varrot, A. / Rognan, D. / Rademacher, C. / Imberty, A. / Titz, A.
History
DepositionApr 14, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 24, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
A: PA-I galactophilic lectin
B: PA-I galactophilic lectin
C: PA-I galactophilic lectin
D: PA-I galactophilic lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,98011
Polymers51,0814
Non-polymers8997
Water4,396244
1
A: PA-I galactophilic lectin
D: PA-I galactophilic lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,1136
Polymers25,5402
Non-polymers5734
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2150 Å2
ΔGint-32 kcal/mol
Surface area10440 Å2
MethodPISA
2
B: PA-I galactophilic lectin
C: PA-I galactophilic lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,8675
Polymers25,5402
Non-polymers3263
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2160 Å2
ΔGint-32 kcal/mol
Surface area10520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.222, 76.066, 107.148
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21221
Components on special symmetry positions
IDModelComponents
11C-303-

HOH

21C-324-

HOH

31C-331-

HOH

41D-331-

HOH

51D-352-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: 0 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: SER / End label comp-ID: SER / Refine code: 0 / Auth seq-ID: 1 - 121 / Label seq-ID: 1 - 121

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22CC
13AA
23DD
14BB
24CC
15BB
25DD
16CC
26DD

NCS ensembles :
ID
1
2
3
4
5
6

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Components

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


Mass: 12770.137 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / 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.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-P4H / [2,4-bis(oxidanyl)phenyl]-[3,4-bis(oxidanyl)phenyl]methanone


Mass: 246.215 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C13H10O5 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 244 / 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: 1.92 Å3/Da / Density % sol: 36.06 %
Crystal growTemperature: 292.15 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 20% PEG6000, 100 mM sodium acetate pH 4.5, 1 M LiCl, 1% DMSO mixed in 1:1 ratio with 10mg/ml of LecA in water containing 100 uM CaCl2. The mixture was deposited onto dried catechol compound ...Details: 20% PEG6000, 100 mM sodium acetate pH 4.5, 1 M LiCl, 1% DMSO mixed in 1:1 ratio with 10mg/ml of LecA in water containing 100 uM CaCl2. The mixture was deposited onto dried catechol compound for co-crystallisation

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9786 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 29, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 1.84→48.22 Å / Num. obs: 35137 / % possible obs: 99.9 % / Redundancy: 13.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.068 / Rpim(I) all: 0.019 / Rrim(I) all: 0.071 / Net I/σ(I): 23.9 / Num. measured all: 472163 / Scaling rejects: 1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.84-1.8813.10.4692750421000.9430.1330.4885.497.9
9-48.2211.30.03415136610.0090.03150.699.5

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.7.2data scaling
REFMAC5.8.0258refinement
PDB_EXTRACT3.25data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1OKO

1oko


Resolution: 1.84→44.01 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.937 / SU B: 3.076 / SU ML: 0.094 / SU R Cruickshank DPI: 0.1703 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.17 / ESU R Free: 0.145
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2255 1776 5.1 %RANDOM
Rwork0.1929 ---
obs0.1945 33319 99.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 75.33 Å2 / Biso mean: 21.196 Å2 / Biso min: 8.8 Å2
Baniso -1Baniso -2Baniso -3
1--0.43 Å2-0 Å20 Å2
2--0.71 Å2-0 Å2
3----0.28 Å2
Refinement stepCycle: final / Resolution: 1.84→44.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3578 0 58 250 3886
Biso mean--38.44 25.85 -
Num. residues----484
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0133772
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173244
X-RAY DIFFRACTIONr_angle_refined_deg1.5451.6335174
X-RAY DIFFRACTIONr_angle_other_deg1.4591.5727548
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0375492
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.50124.97167
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.73615511
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.038158
X-RAY DIFFRACTIONr_chiral_restr0.0720.2490
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.024430
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02758
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A36870.07
12B36870.07
21A36460.09
22C36460.09
31A36020.09
32D36020.09
41B36390.09
42C36390.09
51B35800.09
52D35800.09
61C35980.09
62D35980.09
LS refinement shellResolution: 1.84→1.885 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.26 121 -
Rwork0.232 2380 -
obs--98.04 %

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