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- PDB-6y0v: Fucosylated bicyclic peptide bp71 bound to the fucose binding lec... -

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Basic information

Entry
Database: PDB / ID: 6y0v
TitleFucosylated bicyclic peptide bp71 bound to the fucose binding lectin LecB PA-IIL from Pseudomonas aeruginosa at 1.7 Angstrom resolution
Components
  • Fucose-binding lectin
  • bp71
KeywordsANTIBIOTIC / Antimicrobial / Bicyclic / 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: 1.98 Å
AuthorsBaeriswyl, 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 10, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 24, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2021Group: Database references / Structure summary
Category: citation / citation_author ...citation / citation_author / entity / struct
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _entity.details / _entity.pdbx_description / _struct.pdbx_descriptor / _struct.title
Revision 1.2Feb 2, 2022Group: Database references / Category: citation / citation_author / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.0Feb 1, 2023Group: 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_atoms / pdbx_unobs_or_zero_occ_residues / pdbx_validate_close_contact / struct_asym / struct_conf / struct_conn / struct_ref / 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 / _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.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _struct_conf.beg_auth_seq_id / _struct_conf.beg_label_seq_id / _struct_conf.end_auth_seq_id / _struct_conf.end_label_seq_id / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_ref_seq.ref_id / _struct_ref_seq.seq_align_end
Revision 2.1Feb 7, 2024Group: Data collection / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_conn
Item: _struct_conn.pdbx_leaving_atom_flag
Revision 2.2Oct 16, 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
E: bp71
B: Fucose-binding lectin
C: Fucose-binding lectin
G: bp71
D: Fucose-binding lectin
H: bp71
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,90919
Polymers51,7637
Non-polymers1,14512
Water5,927329
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10660 Å2
ΔGint-131 kcal/mol
Surface area17320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.140, 104.880, 52.996
Angle α, β, γ (deg.)90.000, 93.380, 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: 11734.707 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, C0043_24310, C0044_25260, C0046_23510, CAZ10_21840, CW299_25270, DI492_13230, DT376_00595, PAERUG_E15_London_28_01_14_00983, PAMH19_1713, RW109_RW109_02453
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A069Q9V4, UniProt: Q9HYN5*PLUS
#2: Protein/peptide bp71


Mass: 1608.153 Da / Num. of mol.: 3 / Source method: obtained synthetically / Details: Fucosylated bicyclic peptide bp71 / Source: (synth.) synthetic construct (others)
#3: Chemical
ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 329 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.42 Å3/Da / Density % sol: 49.28 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 0.01 M Cobalt(II) chloride hexahydrate, 0.1 M Sodium acetate trihydrate pH 4.6, 1.0 M 1,6-Hexanediol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.000033 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Dec 17, 2017
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.000033 Å / Relative weight: 1
ReflectionResolution: 1.746→47.235 Å / Num. obs: 89452 / % possible obs: 90.8 % / Redundancy: 1.67 % / Biso Wilson estimate: 26.269 Å2 / CC1/2: 0.998 / Rrim(I) all: 0.089 / Χ2: 0.96 / Net I/σ(I): 5.76
Reflection shellResolution: 1.746→1.755 Å / Redundancy: 1.27 % / Mean I/σ(I) obs: 0.96 / Num. unique obs: 11804 / CC1/2: 0.666 / Rrim(I) all: 0.769 / % possible all: 74.2

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.8 Å47.23 Å
Translation2.8 Å47.23 Å

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Processing

Software
NameVersionClassification
PHENIXv1.11.1-2575refinement
XDSdata reduction
XSCALEdata scaling
PHASER2.8.0phasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1OXC

1oxc


Resolution: 1.98→45.061 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.03 / Phase error: 24.34
RfactorNum. reflection% reflection
Rfree0.2326 3182 5.02 %
Rwork0.1791 --
obs0.1818 63347 93.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 73.94 Å2 / Biso mean: 26.293 Å2 / Biso min: 12.47 Å2
Refinement stepCycle: final / Resolution: 1.98→45.061 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3502 0 60 329 3891
Biso mean--24.79 35.28 -
Num. residues----492
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073600
X-RAY DIFFRACTIONf_angle_d0.7964929
X-RAY DIFFRACTIONf_chiral_restr0.06629
X-RAY DIFFRACTIONf_plane_restr0.004648
X-RAY DIFFRACTIONf_dihedral_angle_d3.4192040
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.9801-2.00960.29981440.2347263896
2.0096-2.0410.29051460.2239275595
2.041-2.07450.29711200.2256235088
2.0745-2.11020.26591400.2161269394
2.1102-2.14860.3161370.2207267296
2.1486-2.18990.25461340.2036261994
2.1899-2.23460.32121340.2023262393
2.2346-2.28320.26271270.1989246089
2.2832-2.33630.25971440.1826268297
2.3363-2.39480.26691450.1727275697
2.3948-2.45950.22511370.1785265497
2.4595-2.53190.26261450.1726271097
2.5319-2.61360.2821430.181267896
2.6136-2.7070.22831400.1732254892
2.707-2.81540.21951390.161270396
2.8154-2.94350.19711400.1625260994
2.9435-3.09860.2141370.1633256092
3.0986-3.29270.17681340.1625259593
3.2927-3.54680.22031390.1512254691
3.5468-3.90360.21281350.1489251191
3.9036-4.4680.21531390.1752263394
4.468-5.62750.18461370.172252791
5.6275-45.0610.23791460.2063264395

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