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- PDB-7nef: Fucosylated linear peptide Fln65 bound to the fucose binding lect... -

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Basic information

Entry
Database: PDB / ID: 7nef
TitleFucosylated linear peptide Fln65 bound to the fucose binding lectin LecB PA-IIL from Pseudomonas aeruginosa at 1.5 Angstrom resolution
Components
  • Fln65
  • Fucose-binding lectin
KeywordsANTIBIOTIC / Antimicrobial peptide / 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 / Fucose-binding lectin / Fucose-binding lectin PA-IIL
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.51 Å
AuthorsPersonne, H. / Baeriswyl, S. / Stocker, A. / Reymond, J.-L.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science Foundation Switzerland
Citation
Journal: Rsc Chem Biol / Year: 2021
Title: A mixed chirality alpha-helix in a stapled bicyclic and a linear antimicrobial peptide revealed by X-ray crystallography.
Authors: Baeriswyl, S. / Personne, H. / Di Bonaventura, I. / Kohler, T. / van Delden, C. / Stocker, A. / Javor, S. / Reymond, J.L.
#1: Journal: Rsc Chem Biol / Year: 2021
Title: A mixed chirality alpha-helix in a stapled bicyclic and a linear antimicrobial peptide revealed by X-ray crystallography.
Authors: Baeriswyl, S. / Personne, H. / Di Bonaventura, I. / Kohler, T. / van Delden, C. / Stocker, A. / Javor, S. / Reymond, J.L.
#2: Journal: Rsc Chem Biol / Year: 2021
Title: A mixed chirality alpha-helix in a stapled bicyclic and a linear antimicrobial peptide revealed by X-ray crystallography.
Authors: Baeriswyl, S. / Personne, H. / Di Bonaventura, I. / Kohler, T. / van Delden, C. / Stocker, A. / Javor, S. / Reymond, J.L.
#3: Journal: Chemrxiv / Year: 2021
Title: Mixed chirality alpha-helix in a stapled bicyclic and a linear antimicrobial peptide revealed by X-ray crystallography
Authors: Personne, H. / Baeriswyl, S. / Di Bonaventura, I. / Kohler, T. / van Delden, C. / Stocker, A. / Javor, S. / Reymond, J.-L.
History
DepositionFeb 3, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 3, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 2, 2022Group: Database references / Category: citation / citation_author / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Jan 31, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / pdbx_initial_refinement_model
Item: _citation.journal_id_ISSN

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fucose-binding lectin
B: Fucose-binding lectin
C: Fucose-binding lectin
D: Fucose-binding lectin
E: Fucose-binding lectin
F: Fucose-binding lectin
G: Fucose-binding lectin
H: Fucose-binding lectin
I: Fln65
J: Fln65
K: Fln65
L: Fln65
M: Fln65
N: Fln65
O: Fln65
P: Fln65
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,81740
Polymers105,52616
Non-polymers2,29124
Water25,4911415
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23150 Å2
ΔGint-295 kcal/mol
Surface area38720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.467, 64.300, 118.926
Angle α, β, γ (deg.)90.000, 94.910, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Fucose-binding lectin / Fucose-binding lectin II (PA-IIL) / Fucose-binding lectin PA-IIL


Mass: 11865.905 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Details: Fucose-binding Lectin LecB PA-IIL from Pseudomonas aeruginosa
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria)
Gene: lecB, C0044_25260, CAZ10_21840, DT376_00595, DY979_15445, ECC04_10105, EFK27_13700, EGV95_09240, EGY23_15550, IPC669_23070, PA5486_01888, PAERUG_E15_London_28_01_14_00983, PAMH19_1713, RW109_RW109_02453
Production host: Escherichia coli BL21 (bacteria) / References: UniProt: A0A069Q9V4, UniProt: Q9HYN5*PLUS
#2: Protein/peptide
Fln65


Mass: 1324.847 Da / Num. of mol.: 8 / Source method: obtained synthetically / Details: Fucosylated linear peptide Fln65 / Source: (synth.) synthetic construct (others)
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 16 / 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.: 8
Source method: isolated from a genetically manipulated source
Formula: C8H14O6
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1415 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.69 Å3/Da / Density % sol: 54.24 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.2M Magnesium formate dihydrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.976 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Nov 2, 2020
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.507→48.591 Å / Num. obs: 336482 / % possible obs: 96.9 % / Redundancy: 3.18 % / CC1/2: 0.997 / Rrim(I) all: 0.117 / Net I/σ(I): 8.23
Reflection shellResolution: 1.51→1.6 Å / Redundancy: 2.36 % / Mean I/σ(I) obs: 0.12 / Num. unique obs: 50384 / CC1/2: 0.685 / Rrim(I) all: 0.933 / % possible all: 89.8

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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: 1.51→48.59 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 0.9 / Phase error: 21.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.206 16718 5.01 %
Rwork0.1821 317222 -
obs0.1833 333940 96.17 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 95.67 Å2 / Biso mean: 21.0708 Å2 / Biso min: 9.11 Å2
Refinement stepCycle: final / Resolution: 1.51→48.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7384 0 16 1415 8815
Biso mean--13.31 31.49 -
Num. residues----1016
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 (%)
1.51-1.520.53263370.55916368670558
1.52-1.540.43484600.41578715917579
1.54-1.560.30885670.2962108531142098
1.56-1.580.29235660.2797107941136099
1.58-1.60.27735780.2672108871146599
1.6-1.620.27055720.2551109461151899
1.62-1.650.25665750.24511100611581100
1.65-1.670.25855760.22541094711523100
1.67-1.70.23555820.22531100611588100
1.7-1.730.2565750.2312108831145899
1.73-1.750.23175820.19941094611528100
1.75-1.790.23475770.19481097011547100
1.79-1.820.21355740.18631094711521100
1.82-1.860.20775710.18171099211563100
1.86-1.90.24855690.2242106511122097
1.9-1.940.34084970.33429388988586
1.94-1.990.19015790.1609109241150399
1.99-2.050.18315730.15121098611559100
2.05-2.110.26675420.2383101951073793
2.11-2.170.16615800.13541096211542100
2.17-2.250.26955460.2188102861083293
2.25-2.340.19555560.1657104191097595
2.34-2.450.14885760.13141093211508100
2.45-2.580.15155810.13331099711578100
2.58-2.740.16435660.1395108411140799
2.74-2.950.1565800.13441095411534100
2.95-3.250.16075770.14151098511562100
3.25-3.720.16095630.1489107341129798
3.72-4.680.18725710.1516107721134398
4.68-48.590.19025700.17109361150699
Refinement TLS params.Method: refined / Origin x: 21.181 Å / Origin y: -7.0985 Å / Origin z: -29.1351 Å
111213212223313233
T0.1128 Å2-0.0025 Å2-0.0027 Å2-0.1197 Å2-0.0009 Å2--0.1435 Å2
L0.0371 °2-0.0068 °2-0.0145 °2-0.0277 °20.0047 °2--0.2014 °2
S0.0091 Å °-0.0085 Å °0.0018 Å °0.005 Å °0.0083 Å °0.0072 Å °0.0047 Å °-0.0043 Å °-0.0145 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA1 - 302
2X-RAY DIFFRACTION1allB1 - 302
3X-RAY DIFFRACTION1allC1 - 302
4X-RAY DIFFRACTION1allD1 - 302
5X-RAY DIFFRACTION1allE1 - 302
6X-RAY DIFFRACTION1allF1 - 302
7X-RAY DIFFRACTION1allG1 - 302
8X-RAY DIFFRACTION1allH1 - 302
9X-RAY DIFFRACTION1allI1 - 13
10X-RAY DIFFRACTION1allJ1 - 13
11X-RAY DIFFRACTION1allK1 - 13
12X-RAY DIFFRACTION1allL1 - 13
13X-RAY DIFFRACTION1allM1 - 13
14X-RAY DIFFRACTION1allN1 - 13
15X-RAY DIFFRACTION1allO1 - 13
16X-RAY DIFFRACTION1allP1 - 13
17X-RAY DIFFRACTION1allS1 - 1415

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