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Basic information

Entry
Database: PDB / ID: 5ney
TitleDiscovery, crystal structures and atomic force microscopy study of thioether ligated D,L-cyclic antimicrobial peptides against multidrug resistant Pseudomonas aeruginosa
Components
  • CYS-TRD-TRP-LYD-LYS-LYD-LYS-LYD-TRP-TRD-CYS-ALA
  • Fucose-binding lectin II (PA-IIL)
KeywordsSUGAR BINDING 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: 1.55 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 / Category: citation / citation_author
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
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection / Derived calculations
Category: atom_site / chem_comp ...atom_site / chem_comp / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _atom_site.occupancy / _chem_comp.type ..._atom_site.occupancy / _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 / _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 2.1Jan 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 2.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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: CYS-TRD-TRP-LYD-LYS-LYD-LYS-LYD-TRP-TRD-CYS-ALA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,87318
Polymers48,6225
Non-polymers1,25213
Water7,080393
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9600 Å2
ΔGint-105 kcal/mol
Surface area16120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.925, 45.748, 103.850
Angle α, β, γ (deg.)90.00, 114.98, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11D-345-

HOH

21D-377-

HOH

31D-389-

HOH

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Components

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Protein / Protein/peptide / Sugars , 3 types, 9 molecules ABCDE

#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
#2: Protein/peptide CYS-TRD-TRP-LYD-LYS-LYD-LYS-LYD-TRP-TRD-CYS-ALA


Mass: 1683.096 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: 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, 402 molecules

#4: Chemical
ChemComp-CA / CALCIUM ION


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


Mass: 106.165 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H10
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 393 / 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: 2.1 Å3/Da / Density % sol: 41.48 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 0.5 M Ammonium Sulfate, 0.1M Sodium citrate tribasic dehydrate, 1.0 M Lithium sulfate monohydrate, pH 5.6

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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: 1.55→47.43 Å / Num. obs: 53265 / % possible obs: 89.6 % / Redundancy: 2.23 % / Rrim(I) all: 0.07 / Net I/σ(I): 12.44
Reflection shellResolution: 1.55→1.64 Å / Mean I/σ(I) obs: 2.58 / Num. unique all: 8356 / CC1/2: 0.754 / Rrim(I) all: 0.532 / % possible all: 87.3

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1OXC

1oxc


Resolution: 1.55→47.428 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.3 / Phase error: 23.02
RfactorNum. reflection% reflection
Rfree0.2173 4725 5.03 %
Rwork0.1847 --
obs0.1863 93968 81.02 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.55→47.428 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3367 0 68 393 3828
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083475
X-RAY DIFFRACTIONf_angle_d1.0524766
X-RAY DIFFRACTIONf_dihedral_angle_d12.5771961
X-RAY DIFFRACTIONf_chiral_restr0.073603
X-RAY DIFFRACTIONf_plane_restr0.005629
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5454-1.5630.3378820.29241550X-RAY DIFFRACTION43
1.563-1.58140.35161600.28573260X-RAY DIFFRACTION87
1.5814-1.60070.3131700.26523195X-RAY DIFFRACTION87
1.6007-1.62090.32971630.2663146X-RAY DIFFRACTION87
1.6209-1.64230.27231760.26383325X-RAY DIFFRACTION88
1.6423-1.66480.30971610.25873118X-RAY DIFFRACTION87
1.6648-1.68850.31591680.25823211X-RAY DIFFRACTION87
1.6885-1.71380.32261670.25333086X-RAY DIFFRACTION86
1.7138-1.74050.26511620.24153173X-RAY DIFFRACTION85
1.7405-1.76910.26511750.22733089X-RAY DIFFRACTION84
1.7691-1.79960.29461530.20992930X-RAY DIFFRACTION81
1.7996-1.83230.25011590.1962937X-RAY DIFFRACTION79
1.8323-1.86750.20161470.19072872X-RAY DIFFRACTION79
1.8675-1.90570.23441500.18442767X-RAY DIFFRACTION75
1.9057-1.94710.21221490.17722906X-RAY DIFFRACTION79
1.9471-1.99240.18611700.16993171X-RAY DIFFRACTION87
1.9924-2.04220.19051720.16713176X-RAY DIFFRACTION86
2.0422-2.09740.24321660.16363218X-RAY DIFFRACTION87
2.0974-2.15920.18971670.16613074X-RAY DIFFRACTION85
2.1592-2.22890.2221630.16323141X-RAY DIFFRACTION86
2.2289-2.30850.21231620.1563118X-RAY DIFFRACTION83
2.3085-2.40090.16941640.15363090X-RAY DIFFRACTION85
2.4009-2.51020.20391680.16893095X-RAY DIFFRACTION84
2.5102-2.64250.23871630.18163044X-RAY DIFFRACTION83
2.6425-2.80810.2091550.16822870X-RAY DIFFRACTION79
2.8081-3.02490.19041480.17772759X-RAY DIFFRACTION76
3.0249-3.32920.20611380.17492587X-RAY DIFFRACTION70
3.3292-3.81080.15921370.17082555X-RAY DIFFRACTION70
3.8108-4.80040.18771520.16742897X-RAY DIFFRACTION79
4.8004-47.45020.22441580.18992883X-RAY DIFFRACTION79

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