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- PDB-8guv: LecA from Pseudomonas aeruginosa in complex with tolcapone (CAS: ... -

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Basic information

Entry
Database: PDB / ID: 8guv
TitleLecA from Pseudomonas aeruginosa in complex with tolcapone (CAS: 134308-13-7)
ComponentsPA-I galactophilic lectin
KeywordsSUGAR BINDING PROTEIN / lectin / glycomimetics / Pseudomonas aeruginosa
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
Tolcapone / PA-I galactophilic lectin
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.32 Å
AuthorsKuhaudomlarp, S. / Siebs, E. / Varrot, A. / Imberty, A. / Titz, A.
Funding support France, Germany, 4items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANR-AAPG-2017 France
Agence Nationale de la Recherche (ANR)ANR-17-CE11-0048 France
German Research Foundation (DFG)Ti756/5-1 Germany
German Research Foundation (DFG)RA1944/7-1 Germany
CitationJournal: To Be Published
Title: LecA from Pseudomonas aeruginosa in complex with tolcapone (CAS: 134308-13-7)
Authors: Siebs, E. / Kuhaudomlarp, S. / Shanina, E. / Varrot, A. / da Silva Fiqueiredo Celestino Gomes, P. / Lerner, C. / Grether, U. / Rademacher, C. / Rognan, D. / Imberty, A. / Titz, A.
History
DepositionSep 13, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 19, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: 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
A: PA-I galactophilic lectin
B: PA-I galactophilic lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,4407
Polymers25,5402
Non-polymers9005
Water4,936274
1
A: PA-I galactophilic lectin
B: PA-I galactophilic lectin
hetero molecules

A: PA-I galactophilic lectin
B: PA-I galactophilic lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,88014
Polymers51,0814
Non-polymers1,80010
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_455-x-1,y,-z+1/21
Unit cell
Length a, b, c (Å)57.650, 164.626, 50.105
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-403-

HOH

21A-485-

HOH

31A-515-

HOH

41B-536-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

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

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

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


Mass: 12770.137 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: LecA was produced as a recombinant protein in E. coli without methionine at position 1.
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: Q05097
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-TCW / Tolcapone / (3,4-dihydroxy-5-nitrophenyl)(4-methylphenyl)methanone


Mass: 273.241 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C14H11NO5 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 274 / 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: 2.33 Å3/Da / Density % sol: 47.15 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 24% PEG 2kMME, 0.1 M KSCN, 0.1 M sodium acetate pH 4.5 cocrystallised with tolcapone.

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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: Apr 8, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 1.32→42.84 Å / Num. obs: 56290 / % possible obs: 99.8 % / Redundancy: 12.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.052 / Rpim(I) all: 0.016 / Rrim(I) all: 0.055 / Net I/σ(I): 25.2
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
1.32-1.3411.10.4512949326610.960.1390.4724.196.4
7.23-42.88.80.05134733930.9950.020.05548.798.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
Aimless0.7.4data scaling
PDB_EXTRACT3.27data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1OKO

1oko


Resolution: 1.32→42.84 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.941 / WRfactor Rfree: 0.2247 / WRfactor Rwork: 0.2062 / FOM work R set: 0.8594 / SU B: 0.84 / SU ML: 0.036 / SU R Cruickshank DPI: 0.0588 / SU Rfree: 0.0602 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.059 / ESU R Free: 0.06 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2222 2793 5 %RANDOM
Rwork0.1987 ---
obs0.1999 53479 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 48.8 Å2 / Biso mean: 14.934 Å2 / Biso min: 7.68 Å2
Baniso -1Baniso -2Baniso -3
1-0.71 Å20 Å2-0 Å2
2---0.75 Å20 Å2
3---0.05 Å2
Refinement stepCycle: final / Resolution: 1.32→42.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1794 0 62 282 2138
Biso mean--23.87 25.68 -
Num. residues----242
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0131940
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171722
X-RAY DIFFRACTIONr_angle_refined_deg1.531.6342667
X-RAY DIFFRACTIONr_angle_other_deg1.4281.5793953
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.85250
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.062584
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.00915259
X-RAY DIFFRACTIONr_dihedral_angle_4_deg4.613154
X-RAY DIFFRACTIONr_chiral_restr0.0670.2248
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022352
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02456
Refine LS restraints NCS

Ens-ID: 1 / Number: 3614 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.11 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.321→1.355 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.326 197 -
Rwork0.304 3833 -
all-4030 -
obs--97.96 %

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