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- PDB-5ngq: Bicyclic antimicrobial peptides -

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Basic information

Entry
Database: PDB / ID: 5ngq
TitleBicyclic antimicrobial peptides
Components
  • DLS-PRO-ALD-CYS-TYD-ALA-CYD-LYS-ALA
  • Fragment of bicycle
  • Fucose-binding lectin II (PA-IIL)
KeywordsSUGAR BINDING PROTEIN / Bycicle / Antimicrobial peptide / Pseudomonas aeruginosa / Biofilm
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
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: 1.17 Å
AuthorsDi Bonaventura, I. / Jin, X. / Visini, R. / Michaud, G. / Robadey, M. / Koehler, T. / van Delden, C. / Stocker, A. / Darbre, T. / Reymond, J.-L.
CitationJournal: Chem Sci / Year: 2017
Title: Chemical space guided discovery of antimicrobial bridged bicyclic peptides against Pseudomonas aeruginosa and its biofilms.
Authors: Di Bonaventura, I. / Jin, X. / Visini, R. / Probst, D. / Javor, S. / Gan, B.H. / Michaud, G. / Natalello, A. / Doglia, S.M. / Kohler, T. / van Delden, C. / Stocker, A. / Darbre, T. / Reymond, J.L.
History
DepositionMar 20, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 23, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2017Group: Advisory / Database references
Category: citation / citation_author / pdbx_unobs_or_zero_occ_atoms
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_PubMed / _citation.title / _citation_author.name
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations
Category: chem_comp / struct_conn ...chem_comp / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _chem_comp.type / _struct_conn.conn_type_id ..._chem_comp.type / _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

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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: DLS-PRO-ALD-CYS-TYD-ALA-CYD-LYS-ALA
F: Fragment of bicycle
G: Fragment of bicycle
H: Fragment of bicycle
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,72820
Polymers49,5828
Non-polymers1,14512
Water8,215456
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: already well known assembly
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)94.708, 45.875, 88.218
Angle α, β, γ (deg.)90.00, 94.21, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-502-

HOH

21C-413-

HOH

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Components

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Protein/peptide , 2 types, 4 molecules EFGH

#2: Protein/peptide DLS-PRO-ALD-CYS-TYD-ALA-CYD-LYS-ALA


Mass: 1039.248 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Protein/peptide Fragment of bicycle


Mass: 534.734 Da / Num. of mol.: 3 / 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 , 2 types, 464 molecules

#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 456 / Source method: isolated from a natural source / Formula: H2O

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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: 1.93 Å3/Da / Density % sol: 36.29 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.1 M sodium acetate trihydrate pH 4.6 and 2.0 M ammonium sulfate.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.99999 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Dec 7, 2015
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99999 Å / Relative weight: 1
ReflectionResolution: 1.17→47.226 Å / Num. obs: 125097 / % possible obs: 97.2 % / Redundancy: 3.1 % / Rrim(I) all: 0.038 / Net I/σ(I): 17.74
Reflection shellResolution: 1.17→1.24 Å / Mean I/σ(I) obs: 3.06 / Num. measured obs: 49037 / Num. unique all: 18095 / CC1/2: 0.907 / Rrim(I) all: 0.359 / % possible all: 87.6

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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: 1.17→47.23 Å / SU ML: 0.1 / Cross valid method: FREE R-VALUE / σ(F): 1.13 / Phase error: 15.43
RfactorNum. reflection% reflection
Rfree0.157 11152 4.99 %
Rwork0.132 --
obs0.134 223602 88.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.17→47.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3359 0 73 456 3888
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093469
X-RAY DIFFRACTIONf_angle_d1.164738
X-RAY DIFFRACTIONf_dihedral_angle_d13.9131142
X-RAY DIFFRACTIONf_chiral_restr0.119599
X-RAY DIFFRACTIONf_plane_restr0.007629
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.1659-1.17920.28371990.24543777X-RAY DIFFRACTION47
1.1792-1.19310.2383370.21486344X-RAY DIFFRACTION79
1.1931-1.20760.24113290.20736444X-RAY DIFFRACTION81
1.2076-1.22290.23013480.1976558X-RAY DIFFRACTION82
1.2229-1.2390.23393460.19346620X-RAY DIFFRACTION82
1.239-1.2560.22013500.17866720X-RAY DIFFRACTION84
1.256-1.27390.20153490.16766744X-RAY DIFFRACTION84
1.2739-1.29290.19633610.15976827X-RAY DIFFRACTION86
1.2929-1.31310.18093510.15276878X-RAY DIFFRACTION85
1.3131-1.33470.18963670.14796910X-RAY DIFFRACTION87
1.3347-1.35770.17583690.15426969X-RAY DIFFRACTION87
1.3577-1.38240.18423630.1427023X-RAY DIFFRACTION87
1.3824-1.4090.17563700.1376998X-RAY DIFFRACTION88
1.409-1.43770.17143720.12477158X-RAY DIFFRACTION90
1.4377-1.4690.15513800.12357383X-RAY DIFFRACTION91
1.469-1.50320.16213920.12087377X-RAY DIFFRACTION92
1.5032-1.54070.15953880.11067309X-RAY DIFFRACTION92
1.5407-1.58240.14673960.10437480X-RAY DIFFRACTION93
1.5824-1.6290.1383990.10187466X-RAY DIFFRACTION93
1.629-1.68160.12833930.10457395X-RAY DIFFRACTION93
1.6816-1.74170.15694010.10937490X-RAY DIFFRACTION93
1.7417-1.81140.14113900.10787438X-RAY DIFFRACTION93
1.8114-1.89380.13973850.10717444X-RAY DIFFRACTION93
1.8938-1.99370.12723940.10447613X-RAY DIFFRACTION95
1.9937-2.11860.13114010.11017629X-RAY DIFFRACTION96
2.1186-2.28220.13514070.11977658X-RAY DIFFRACTION96
2.2822-2.51180.14723940.12497637X-RAY DIFFRACTION95
2.5118-2.87520.16074050.14477698X-RAY DIFFRACTION96
2.8752-3.62230.15133990.13997523X-RAY DIFFRACTION94
3.6223-47.26490.16784170.14957940X-RAY DIFFRACTION99

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