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- PDB-8anr: Fucosylated alternate chirality linear peptide FHP30 bound to the... -

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Basic information

Entry
Database: PDB / ID: 8anr
TitleFucosylated alternate chirality linear peptide FHP30 bound to the fucose binding lectin LecB PA-IIL from Pseudomonas aeruginosa at 1.6 Angstrom resolution.
Components
  • Fucose-binding lectin PA-IIL
  • Fucosylated mixed-chirality linear peptide FHP30
KeywordsANTIBIOTIC / Antimicrobial peptide / alpha helix / mixed-chirality / fucose-binding lectin
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: 1.62 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 5, 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 1.4Nov 6, 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: Fucosylated mixed-chirality linear peptide FHP30
D: Fucosylated mixed-chirality linear peptide FHP30
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,68810
Polymers26,1154
Non-polymers5736
Water4,756264
1
A: Fucose-binding lectin PA-IIL
C: Fucosylated mixed-chirality linear peptide FHP30
hetero molecules

A: Fucose-binding lectin PA-IIL
C: Fucosylated mixed-chirality linear peptide FHP30
hetero molecules

B: Fucose-binding lectin PA-IIL
D: Fucosylated mixed-chirality linear peptide FHP30
hetero molecules

B: Fucose-binding lectin PA-IIL
D: Fucosylated mixed-chirality linear peptide FHP30
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,37620
Polymers52,2308
Non-polymers1,14512
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-x,-y-1,z1
crystal symmetry operation3_445-y-1/2,x-1/2,z+1/21
crystal symmetry operation4_545y+1/2,-x-1/2,z+1/21
Unit cell
Length a, b, c (Å)70.691, 70.691, 103.398
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number94
Space group name H-MP42212
Components on special symmetry positions
IDModelComponents
11B-444-

HOH

21B-483-

HOH

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Components

#1: Protein Fucose-binding lectin PA-IIL


Mass: 11734.707 Da / Num. of mol.: 2
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 Fucosylated mixed-chirality linear peptide FHP30


Mass: 1322.833 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / 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.: 2 / Source method: obtained synthetically / Formula: C8H14O6 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 264 / 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: 2.44 Å3/Da / Density % sol: 49.55 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.2 M Ammonium citrate tribasic pH 7.0, 20% 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: 1.618→45 Å / Num. obs: 63963 / % possible obs: 100 % / Redundancy: 13.85 % / CC1/2: 0.999 / Rrim(I) all: 0.152 / Net I/σ(I): 15.46
Reflection shellResolution: 1.618→1.626 Å / Redundancy: 13.43 % / Mean I/σ(I) obs: 0.98 / Num. unique obs: 10328 / CC1/2: 0.378 / % possible all: 99.9

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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: 1.62→45 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 18.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1834 1709 5 %
Rwork0.1482 32456 -
obs0.15 34165 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 83.09 Å2 / Biso mean: 27.4004 Å2 / Biso min: 14.63 Å2
Refinement stepCycle: final / Resolution: 1.62→45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1866 0 4 264 2134
Biso mean--20.92 38.63 -
Num. residues----254
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.62-1.670.27291390.223826392778
1.67-1.720.27981400.218326612801
1.72-1.780.2721390.18826432782
1.78-1.850.24611410.171626772818
1.85-1.940.20611390.146426412780
1.94-2.040.19091410.129126882829
2.04-2.170.19211420.130826902832
2.17-2.330.18891420.129626812823
2.33-2.570.17841410.132627132854
2.57-2.940.16191450.141327362881
2.94-3.70.161460.138727672913
3.7-450.171540.157629203074

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