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- PDB-8an9: Fucosylated mixed-chirality linear peptide FHP5 bound to the fuco... -

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Basic information

Entry
Database: PDB / ID: 8an9
TitleFucosylated mixed-chirality linear peptide FHP5 bound to the fucose binding lectin LecB PA-IIL from Pseudomonas aeruginosa at 1.3 Angstrom resolution.
Components
  • Fucose-binding lectin PA-IIL
  • Mixed-chirality peptide FHP5
KeywordsANTIBIOTIC / Antimicrobial peptide / alpha helix / mixed-chirality
Function / homologyLectin, sugar-binding / Calcium-mediated lectin / Calcium-mediated lectin superfamily / Fucose-binding lectin II (PA-IIL) / single-species biofilm formation / carbohydrate binding / metal ion binding / Chem-ZDC / Fucose-binding lectin PA-IIL
Function and homology information
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.273 Å
AuthorsPersonne, H. / Stocker, A. / Reymond, J.-L.
Funding supportEuropean Union, Switzerland, 2items
OrganizationGrant numberCountry
European Research Council (ERC)885076European 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 4, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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: Mixed-chirality peptide FHP5
F: Mixed-chirality peptide FHP5
G: Mixed-chirality peptide FHP5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,05619
Polymers50,9107
Non-polymers1,14512
Water8,683482
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10650 Å2
ΔGint-130 kcal/mol
Surface area17490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.766, 62.783, 64.226
Angle α, β, γ (deg.)90.000, 92.820, 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) / Gene: lecB, PA3361 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q9HYN5
#2: Protein/peptide Mixed-chirality peptide FHP5


Mass: 1323.840 Da / Num. of mol.: 3 / 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.: 482 / 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: 2.13 Å3/Da / Density % sol: 42.16 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.1 M HEPES pH 7.5, 20% Jeffamine M-600

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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: 1.273→44.87 Å / Num. obs: 211407 / % possible obs: 96.9 % / Redundancy: 1.03 % / CC1/2: 0.998 / Rrim(I) all: 0.069 / Net I/σ(I): 9.16
Reflection shellResolution: 1.273→1.279 Å / Redundancy: 2.4 % / Mean I/σ(I) obs: 1.08 / Num. unique obs: 32349 / CC1/2: 0.717 / Rrim(I) all: 0.841 / % possible all: 41.7

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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: 1.273→44.87 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 20.81 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1919 5421 5 %
Rwork0.1627 102993 -
obs0.1642 108414 98.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 99.32 Å2 / Biso mean: 23.2965 Å2 / Biso min: 11.41 Å2
Refinement stepCycle: final / Resolution: 1.273→44.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3518 0 45 482 4045
Biso mean--32.74 33.68 -
Num. residues----480
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.273-1.290.28711400.288265876
1.29-1.30.29691780.2609337999
1.3-1.320.28551830.25173471100
1.32-1.330.24661810.24073449100
1.33-1.350.28121820.23593443100
1.35-1.370.28461810.2213440100
1.37-1.390.23711840.20613497100
1.39-1.410.26191790.20743413100
1.41-1.430.24291820.18763457100
1.43-1.460.21891810.18983451100
1.46-1.480.2391820.18643468100
1.48-1.510.22871830.18353461100
1.51-1.540.22521810.17353437100
1.54-1.570.19851830.17013486100
1.57-1.60.21751850.16093505100
1.6-1.640.20431800.17163434100
1.64-1.680.20531820.16323448100
1.68-1.730.18891820.16213451100
1.73-1.780.17881820.1573470100
1.78-1.840.17881830.15173468100
1.84-1.90.16841820.15633460100
1.9-1.980.17581820.1553459100
1.98-2.070.18851810.1524343099
2.07-2.180.19281820.1487345899
2.18-2.310.19171830.1492347199
2.31-2.490.19921810.1533344099
2.49-2.740.17891830.15063475100
2.74-3.140.16081820.15123492100
3.14-3.950.16391840.1424347799
3.95-44.870.19231870.171354599

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