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Basic information

Entry
Database: PDB / ID: 5nes
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
  • 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
1,3-dimethylbenzene / 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: 1.606 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 11, 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 1.2Jul 29, 2020Group: Data collection / Derived calculations
Category: chem_comp / pdbx_struct_conn_angle ...chem_comp / pdbx_struct_conn_angle / 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.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_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 1.4Nov 20, 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)
E: CYD-TRP-TRD-LYS-LYD-LYS-LYD-LYS-TRD-TRP-CYD
B: Fucose-binding lectin II (PA-IIL)
C: Fucose-binding lectin II (PA-IIL)
D: Fucose-binding lectin II (PA-IIL)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,80318
Polymers48,5525
Non-polymers1,25213
Water10,305572
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry, Protein already known as tetrameric and our own production checked with mass spectroscopy.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12470 Å2
ΔGint-134 kcal/mol
Surface area15210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.201, 48.527, 52.562
Angle α, β, γ (deg.)84.92, 79.98, 80.61
Int Tables number1
Space group name H-MP1

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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 CYD-TRP-TRD-LYS-LYD-LYS-LYD-LYS-TRD-TRP-CYD


Mass: 1613.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#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 genetically manipulated source
Formula: C8H14O6

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Non-polymers , 3 types, 581 molecules

#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-8VH / 1,3-dimethylbenzene


Mass: 106.165 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H10
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 572 / 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: 2.27 Å3/Da / Density % sol: 45.76 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.005 M Cobalt(II) chloride hexahydrate, 0.1M HEPES, 12% Polyethylene glycol 3350,

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.03679 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Aug 20, 2016
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03679 Å / Relative weight: 1
ReflectionResolution: 1.606→47.784 Å / Num. obs: 51247 / % possible obs: 90.6 % / Redundancy: 1.78 % / Rrim(I) all: 0.032 / Net I/σ(I): 23.48
Reflection shellResolution: 1.606→1.7 Å / Mean I/σ(I) obs: 11.32 / Num. unique all: 7617 / CC1/2: 0.99 / % possible all: 82.9

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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: 1.606→47.784 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 2.02 / Phase error: 15.61
RfactorNum. reflection% reflection
Rfree0.164 2561 5 %
Rwork0.1425 --
obs0.1436 51247 90.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.606→47.784 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3365 0 68 572 4005
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073475
X-RAY DIFFRACTIONf_angle_d0.9184770
X-RAY DIFFRACTIONf_dihedral_angle_d12.7391950
X-RAY DIFFRACTIONf_chiral_restr0.064603
X-RAY DIFFRACTIONf_plane_restr0.004627
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6058-1.63670.21891050.15392015X-RAY DIFFRACTION67
1.6367-1.67010.18541450.15782756X-RAY DIFFRACTION91
1.6701-1.70650.18891420.15572715X-RAY DIFFRACTION91
1.7065-1.74620.18531450.16432754X-RAY DIFFRACTION92
1.7462-1.78980.18551450.15142746X-RAY DIFFRACTION92
1.7898-1.83820.19861420.15012703X-RAY DIFFRACTION91
1.8382-1.89230.17331460.14832780X-RAY DIFFRACTION93
1.8923-1.95340.16671470.14162777X-RAY DIFFRACTION93
1.9534-2.02320.1751460.1362777X-RAY DIFFRACTION92
2.0232-2.10420.15191450.13312744X-RAY DIFFRACTION92
2.1042-2.20.15581450.12812750X-RAY DIFFRACTION92
2.2-2.3160.15211430.12842719X-RAY DIFFRACTION92
2.316-2.46110.16741420.14012711X-RAY DIFFRACTION91
2.4611-2.65110.17741460.14542761X-RAY DIFFRACTION91
2.6511-2.91780.16541410.14362694X-RAY DIFFRACTION91
2.9178-3.33990.18491480.14622795X-RAY DIFFRACTION93
3.3399-4.20760.12891450.13672769X-RAY DIFFRACTION93
4.2076-47.80560.1421430.14542720X-RAY DIFFRACTION91

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