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- PDB-7new: Fucosylated heterochiral linear peptide Fdln69 bound to the fucos... -

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Entry
Database: PDB / ID: 7new
TitleFucosylated heterochiral linear peptide Fdln69 bound to the fucose binding lectin LecB PA-IIL from Pseudomonas aeruginosa at 2.0 Angstrom resolution
Components
  • Fucose-binding lectin
  • Heterochiral peptide Fdln69
KeywordsANTIBIOTIC / Antimicrobial peptide / Lectin / ANTIMICROBIAL PROTEIN
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 / Fucose-binding lectin PA-IIL
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.02 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 5, 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 2.0Dec 21, 2022Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / citation / entity / entity_poly / entity_poly_seq / pdbx_entity_nonpoly / pdbx_entity_src_syn / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_residues / pdbx_validate_close_contact / pdbx_validate_symm_contact / struct_asym / struct_conf / struct_conn / struct_ref_seq
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.group_PDB / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.label_seq_id / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.pdbx_label_seq_id / _atom_site_anisotrop.type_symbol / _citation.journal_id_ISSN / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _pdbx_unobs_or_zero_occ_residues.label_seq_id / _struct_conf.beg_label_seq_id / _struct_conf.end_label_seq_id / _struct_ref_seq.db_align_beg / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.seq_align_end
Revision 2.1Jan 31, 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
B: Fucose-binding lectin
C: Fucose-binding lectin
D: Fucose-binding lectin
E: Heterochiral peptide Fdln69
G: Heterochiral peptide Fdln69
H: Heterochiral peptide Fdln69
F: Heterochiral peptide Fdln69
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,90820
Polymers52,7638
Non-polymers1,14512
Water4,252236
1
A: Fucose-binding lectin
B: Fucose-binding lectin
G: Heterochiral peptide Fdln69
F: Heterochiral peptide Fdln69
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,95410
Polymers26,3824
Non-polymers5736
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Fucose-binding lectin
D: Fucose-binding lectin
E: Heterochiral peptide Fdln69
H: Heterochiral peptide Fdln69
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,95410
Polymers26,3824
Non-polymers5736
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)130.586, 64.786, 73.632
Angle α, β, γ (deg.)90.000, 113.330, 90.000
Int Tables number5
Space group name H-MC121

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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.: 4
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(DE3) (bacteria) / References: UniProt: A0A069Q9V4, UniProt: Q9HYN5*PLUS
#2: Polypeptide(D)
Heterochiral peptide Fdln69


Mass: 1324.847 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: Fucosylated heterochiral linear peptide Fdln69 / 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 / Details: Fucosylated heterochiral linear peptide Fdln69 / Source: (synth.) synthetic construct (others)
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 236 / 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: 2.81 Å3/Da / Density % sol: 56.17 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2M Sodium citrate tribasic dihydrate, 0.1M Sodium cacodylate trihydrate pH 6.5, 30% v/v 2-Propanol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.976437 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: 0.976437 Å / Relative weight: 1
ReflectionResolution: 2.017→48.288 Å / Num. obs: 71291 / % possible obs: 97.5 % / Redundancy: 3.55 % / CC1/2: 0.995 / Rrim(I) all: 0.167 / Net I/σ(I): 6.89
Reflection shellResolution: 2.02→2.14 Å / Redundancy: 3.48 % / Mean I/σ(I) obs: 1.01 / Num. unique obs: 11367 / CC1/2: 0.512 / % possible all: 96.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIXv1.17refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1OXC

1oxc


Resolution: 2.02→40.03 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.32 / Phase error: 27.17 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.228 3545 4.98 %
Rwork0.207 67660 -
obs0.208 71205 97.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 161.23 Å2 / Biso mean: 43.0425 Å2 / Biso min: 25.46 Å2
Refinement stepCycle: final / Resolution: 2.02→40.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3510 0 63 236 3809
Biso mean--62.75 46.32 -
Num. residues----480
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 25

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.02-2.040.3651380.3772586272494
2.04-2.070.36851390.37992665280496
2.07-2.10.41291410.37252680282197
2.1-2.140.35021440.33282746289097
2.14-2.170.29861400.31582657279797
2.17-2.210.34991410.30042713285497
2.21-2.250.33811410.29582679282097
2.25-2.290.29961440.28092693283797
2.29-2.340.28151400.26092695283597
2.34-2.390.2581430.24382711285498
2.39-2.450.28751420.24782741288398
2.45-2.510.29021370.25082685282298
2.51-2.580.25221440.22842725286998
2.58-2.650.22621410.22632706284798
2.65-2.740.24341410.20792717285898
2.74-2.840.24061390.20042722286198
2.84-2.950.19151430.18882751289498
2.95-3.080.19931410.19242719286098
3.08-3.240.21961420.18622708285098
3.25-3.450.21931440.17022726287098
3.45-3.710.19171440.1522714285898
3.71-4.090.18511470.16462759290698
4.09-4.680.17811450.16292701284698
4.68-5.890.20081420.1742710285298
5.89-40.030.18851420.19972751289399
Refinement TLS params.Method: refined / Origin x: 26.2953 Å / Origin y: 8.6788 Å / Origin z: 17.1692 Å
111213212223313233
T0.3638 Å20.0043 Å20.0396 Å2-0.278 Å20.0049 Å2--0.3178 Å2
L0.3489 °2-0.0622 °2-0.2762 °2-0.9457 °20.0802 °2--0.796 °2
S-0.0127 Å °0.0165 Å °-0.0669 Å °-0.0069 Å °-0.0084 Å °0.0259 Å °-0.027 Å °-0.0109 Å °-0.0001 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 - 13
6X-RAY DIFFRACTION1allF1 - 2
7X-RAY DIFFRACTION1allG1 - 13
8X-RAY DIFFRACTION1allH1 - 3
9X-RAY DIFFRACTION1allS1 - 236

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