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- PDB-8aoo: Fucosylated mixed-chirality linear peptide FHP31 bound to the fuc... -

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Basic information

Entry
Database: PDB / ID: 8aoo
TitleFucosylated mixed-chirality linear peptide FHP31 bound to the fucose binding lectin LecB PA-IIL from Pseudomonas aeruginosa at 1.2 Angstrom resolution.
Components
  • Fucose-binding lectin PA-IIL
  • Fucosylated mixed-chirality peptide FHP31
KeywordsANTIBIOTIC / Antimicrobial peptide / mixed-chirality / fucose-binding lectin
Function / homology
Function and homology information


single-species biofilm formation / carbohydrate binding / metal ion binding
Similarity search - Function
Lectin, sugar-binding / Calcium-mediated lectin / Calcium-mediated lectin superfamily / Fucose-binding lectin II (PA-IIL)
Similarity search - Domain/homology
Chem-ZDC / polypeptide(D) / polypeptide(D) (> 10) / Fucose-binding lectin PA-IIL
Similarity search - Component
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.18 Å
AuthorsPersonne, H. / Stocker, A. / Reymond, J.-L.
Funding supportEuropean Union, Switzerland, 2items
OrganizationGrant numberCountry
European Research Council (ERC)European Union
Swiss National Science Foundation Switzerland
CitationJournal: J.Med.Chem. / Year: 2023
Title: To Fold or Not to Fold: Diastereomeric Optimization of an alpha-Helical Antimicrobial Peptide.
Authors: Personne, H. / Paschoud, T. / Fulgencio, S. / Baeriswyl, S. / Kohler, T. / van Delden, C. / Stocker, A. / Javor, S. / Reymond, J.L.
History
DepositionAug 8, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 31, 2023Provider: repository / Type: Initial release
Revision 1.1Jun 7, 2023Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jun 21, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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: Fucosylated mixed-chirality peptide FHP31
F: Fucosylated mixed-chirality peptide FHP31
H: Fucosylated mixed-chirality peptide FHP31
I: Fucosylated mixed-chirality peptide FHP31
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,37620
Polymers52,2308
Non-polymers1,14512
Water11,602644
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10850 Å2
ΔGint-143 kcal/mol
Surface area18450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.777, 62.670, 64.407
Angle α, β, γ (deg.)90.000, 93.190, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Fucose-binding lectin PA-IIL


Mass: 11734.707 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria)
Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1
Gene: lecB, PA3361 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q9HYN5
#2: Polypeptide(D)
Fucosylated mixed-chirality peptide FHP31


Mass: 1322.833 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca
#4: Sugar
ChemComp-ZDC / 3,7-anhydro-2,8-dideoxy-L-glycero-D-gluco-octonic acid


Type: D-saccharide / Mass: 206.193 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H14O6 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 644 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.06 Å3/Da / Density % sol: 40.2 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 M Ammonium acetate, 0.1 M HEPES pH 7.5, 25% w/v polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.000023 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Dec 13, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.000023 Å / Relative weight: 1
ReflectionResolution: 1.18→44.88 Å / Num. obs: 235325 / % possible obs: 86.5 % / Redundancy: 1.16 % / CC1/2: 0.999 / Rrim(I) all: 0.044 / Net I/σ(I): 20.68
Reflection shellResolution: 1.18→1.19 Å / Mean I/σ(I) obs: 2.48 / Num. unique obs: 15432 / CC1/2: 0.812 / Rrim(I) all: 0.465 / % possible all: 35

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1OXC

1oxc


Resolution: 1.18→44.88 Å / SU ML: 0.07 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 14.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1514 6214 5 %
Rwork0.1268 118054 -
obs0.1281 124268 90.09 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 60.13 Å2 / Biso mean: 15.382 Å2 / Biso min: 6.46 Å2
Refinement stepCycle: final / Resolution: 1.18→44.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3549 0 63 644 4256
Biso mean--26.01 26.11 -
Num. residues----480
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.18-1.190.2929400.269775779717
1.19-1.210.2337930.22411781187441
1.21-1.220.23571250.20982375250055
1.22-1.240.20521450.18082760290563
1.24-1.250.20341700.1613230340074
1.25-1.270.21741880.15533550373882
1.27-1.290.18682030.13673861406488
1.29-1.310.16862150.12824088430394
1.31-1.330.15822190.11864154437396
1.33-1.350.15282220.11794225444797
1.35-1.370.14972240.1184263448798
1.37-1.40.13282270.11084310453799
1.4-1.420.15732310.108943864617100
1.42-1.450.14872270.106743094536100
1.45-1.490.13912280.11143404568100
1.49-1.520.14382310.108143844615100
1.52-1.560.13932280.106843254553100
1.56-1.60.13122310.106143974628100
1.6-1.650.15122290.110843544583100
1.65-1.70.14822300.119443584588100
1.7-1.760.15632300.119543684598100
1.76-1.830.14572300.122443644594100
1.83-1.910.14092290.120643504579100
1.91-2.020.12512300.113143714601100
2.02-2.140.13232290.120143494578100
2.14-2.310.1292310.124243984629100
2.31-2.540.15732290.132743454574100
2.54-2.910.16292320.137344154647100
2.91-3.660.15292320.129843984630100
3.66-44.880.16022360.140144894725100

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