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Basic information

Entry
Database: PDB / ID: 5nf0
TitleDiscovery, crystal structures and atomic force microscopy study of thioether ligated D,L-cyclic antimicrobial peptides against multidrug resistant Pseudomonas aeruginosa
Components
  • CYD-TRP-TRD-LYS-LYD-LYS-LYD-LYS-TRD-TRP-CYD-GLY
  • Fragment of ligand
  • Fucose-binding lectin II (PA-IIL)
KeywordsANTIMICROBIAL PROTEIN / Cyclic peptides / Antimicrobials / Pseudomonas aeruginosa
Function / homology
Function and homology information


single-species biofilm formation / carbohydrate binding / metal ion binding
Similarity search - Function
Calcium-mediated lectin / Lectin, sugar-binding / Calcium-mediated lectin / Calcium-mediated lectin superfamily / Fucose-binding lectin II (PA-IIL) / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
ORTHO-XYLENE / 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 / Resolution: 1.271 Å
AuthorsReymond, J.-L. / Darbre, T. / Stocker, A. / Hong, W. / van Delden, C. / Koehler, T. / Luscher, A. / Visini, R. / Fu, Y. / Di Bonaventura, I. / He, R.
CitationJournal: Chem Sci / Year: 2017
Title: Design, crystal structure and atomic force microscopy study of thioether ligated d,l-cyclic antimicrobial peptides against multidrug resistant Pseudomonas aeruginosa.
Authors: He, R. / Di Bonaventura, I. / Visini, R. / Gan, B.H. / Fu, Y. / Probst, D. / Luscher, A. / Kohler, T. / van Delden, C. / Stocker, A. / Hong, W. / Darbre, T. / Reymond, J.L.
History
DepositionMar 13, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 13, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 6, 2017Group: Database references / Derived calculations
Category: citation / citation_author / pdbx_struct_assembly_gen
Item: _citation.journal_id_ISSN / _citation.journal_volume ..._citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name / _pdbx_struct_assembly_gen.asym_id_list
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations / Refinement description
Category: chem_comp / pdbx_struct_conn_angle ...chem_comp / pdbx_struct_conn_angle / refine_hist / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _chem_comp.type / _pdbx_struct_conn_angle.ptnr1_auth_asym_id ..._chem_comp.type / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _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_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_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_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _refine_hist.d_res_low / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.0Oct 1, 2025Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / pdbx_database_status ...atom_site / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / struct_asym / struct_conn / struct_sheet / struct_sheet_order / struct_sheet_range
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.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _pdbx_database_status.pdb_format_compatible / _pdbx_nonpoly_scheme.asym_id / _pdbx_nonpoly_scheme.auth_mon_id / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_nonpoly_scheme.entity_id / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.ndb_seq_num / _pdbx_nonpoly_scheme.pdb_mon_id / _pdbx_nonpoly_scheme.pdb_seq_num / _pdbx_nonpoly_scheme.pdb_strand_id / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _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_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_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_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_asym.entity_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fucose-binding lectin II (PA-IIL)
B: Fucose-binding lectin II (PA-IIL)
C: Fucose-binding lectin II (PA-IIL)
D: Fucose-binding lectin II (PA-IIL)
E: CYD-TRP-TRD-LYS-LYD-LYS-LYD-LYS-TRD-TRP-CYD-GLY
F: Fragment of ligand
G: CYD-TRP-TRD-LYS-LYD-LYS-LYD-LYS-TRD-TRP-CYD-GLY
H: CYD-TRP-TRD-LYS-LYD-LYS-LYD-LYS-TRD-TRP-CYD-GLY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,53923
Polymers52,0758
Non-polymers1,46415
Water10,647591
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: already known by first crystallization. Well known protein in literature
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11630 Å2
ΔGint-82 kcal/mol
Surface area18300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.278, 99.966, 106.611
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein/peptide , 2 types, 4 molecules EGHF

#2: Protein/peptide CYD-TRP-TRD-LYS-LYD-LYS-LYD-LYS-TRD-TRP-CYD-GLY


Mass: 1611.033 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Protein/peptide Fragment of ligand


Mass: 303.274 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Protein / Sugars , 2 types, 8 molecules ABCD

#1: Protein
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
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria)
Gene: lecB, PAERUG_E15_London_28_01_14_00983, PAERUG_P32_London_17_VIM_2_10_11_00423, PAMH19_1713
Production host: Escherichia coli (E. coli) / References: UniProt: A0A069Q9V4, UniProt: Q9HYN5*PLUS
#5: 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 genetically manipulated source
Formula: C8H14O6

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Non-polymers , 3 types, 602 molecules

#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca
#6: Chemical ChemComp-OXE / ORTHO-XYLENE


Mass: 106.165 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H10
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 591 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.31 Å3/Da / Density % sol: 46.72 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.005 M Cadmium chloride hydrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.00003 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jun 29, 2016
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00003 Å / Relative weight: 1
ReflectionResolution: 1.27→47.03 Å / Num. obs: 120367 / % possible obs: 94.1 % / Redundancy: 3.31 % / Rrim(I) all: 0.058 / Net I/σ(I): 13.95
Reflection shellResolution: 1.27→1.35 Å / Mean I/σ(I) obs: 2.2 / Num. unique all: 18173 / Num. unique obs: 58803 / CC1/2: 0.851 / Rrim(I) all: 0.615 / % possible all: 88.8

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1OXC

1oxc


Resolution: 1.271→47.03 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.15 / Phase error: 19.46 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1845 11349 5.01 %
Rwork0.1628 --
obs0.1639 226635 92.08 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.271→47.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3628 0 84 591 4303
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0113774
X-RAY DIFFRACTIONf_angle_d1.265150
X-RAY DIFFRACTIONf_dihedral_angle_d14.3231210
X-RAY DIFFRACTIONf_chiral_restr0.126625
X-RAY DIFFRACTIONf_plane_restr0.008662
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.271-1.28550.30913390.28296373X-RAY DIFFRACTION81
1.2855-1.30060.25183550.27626665X-RAY DIFFRACTION86
1.3006-1.31640.29343640.26526801X-RAY DIFFRACTION88
1.3164-1.33310.29723680.25776923X-RAY DIFFRACTION88
1.3331-1.35070.29693510.26046775X-RAY DIFFRACTION88
1.3507-1.36920.28653490.25436655X-RAY DIFFRACTION85
1.3692-1.38870.24833600.23756800X-RAY DIFFRACTION88
1.3887-1.40940.24883620.22556865X-RAY DIFFRACTION87
1.4094-1.43150.23863650.21896962X-RAY DIFFRACTION90
1.4315-1.45490.26343730.21977074X-RAY DIFFRACTION90
1.4549-1.480.20813730.20597163X-RAY DIFFRACTION92
1.48-1.50690.20563790.20297156X-RAY DIFFRACTION92
1.5069-1.53590.20883790.18357254X-RAY DIFFRACTION93
1.5359-1.56730.20573880.17457313X-RAY DIFFRACTION93
1.5673-1.60140.19883790.1657237X-RAY DIFFRACTION94
1.6014-1.63860.16663900.16337436X-RAY DIFFRACTION94
1.6386-1.67960.1853880.15857358X-RAY DIFFRACTION94
1.6796-1.7250.19223900.16127408X-RAY DIFFRACTION95
1.725-1.77580.20363910.1557319X-RAY DIFFRACTION94
1.7758-1.83310.17183730.1517026X-RAY DIFFRACTION90
1.8331-1.89860.17953890.1477319X-RAY DIFFRACTION94
1.8986-1.97460.15923910.13357403X-RAY DIFFRACTION95
1.9746-2.06450.14553920.13167546X-RAY DIFFRACTION97
2.0645-2.17330.15234000.13377536X-RAY DIFFRACTION97
2.1733-2.30950.17073940.14527494X-RAY DIFFRACTION96
2.3095-2.48780.19714030.15067536X-RAY DIFFRACTION97
2.4878-2.73820.1533930.1547552X-RAY DIFFRACTION97
2.7382-3.13430.17463860.15467293X-RAY DIFFRACTION93
3.1343-3.94860.1713780.14277374X-RAY DIFFRACTION95
3.9486-47.06840.16014070.15267670X-RAY DIFFRACTION98

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