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- PDB-5i8m: Bicyclic antimibrocial peptides -

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Basic information

Entry
Database: PDB / ID: 5i8m
TitleBicyclic antimibrocial peptides
Components
  • DLS-LYS-CYS-LYS-LEU-CYS-LEU-LYS-NH2
  • Fucose-binding lectin
KeywordsSUGAR BINDING PROTEIN / Bicycle / Antimicrobial peptide / pseudomonas aeruginosa / biofilm
Function / homology
Function and homology information


single-species biofilm formation / carbohydrate 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: 2.13 Å
AuthorsDi Bonaventura, I. / Jin, X. / Visini, R. / Michaud, G. / Robadey, M. / Koehler, T. / van Delden, C. / Stocker, A. / Darbre, T. / Reymond, J.-L.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science Foundation Switzerland
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
DepositionFeb 19, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Aug 23, 2017Provider: repository / Type: Initial release
Revision 2.0Sep 13, 2017Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Derived calculations
Category: atom_site / pdbx_audit_support ...atom_site / pdbx_audit_support / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_site / struct_site_gen
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_audit_support.funding_organization / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_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_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_unobs_or_zero_occ_atoms.auth_asym_id / _pdbx_unobs_or_zero_occ_atoms.auth_seq_id / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _struct_conn.pdbx_dist_value / _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.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_site.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_seq_id / _struct_site_gen.auth_asym_id / _struct_site_gen.auth_seq_id / _struct_site_gen.label_asym_id
Revision 2.1Nov 29, 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_PubMed / _citation.title / _citation_author.name
Revision 2.2Jul 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 2.3Jan 10, 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
B: Fucose-binding lectin
C: Fucose-binding lectin
D: Fucose-binding lectin
E: DLS-LYS-CYS-LYS-LEU-CYS-LEU-LYS-NH2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,13317
Polymers47,9875
Non-polymers1,14512
Water4,324240
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8070 Å2
ΔGint-107 kcal/mol
Surface area17400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.309, 79.365, 52.584
Angle α, β, γ (deg.)90.00, 94.46, 90.00
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 / Photopexin A


Mass: 11734.707 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria)
Gene: lecB, AN280_27645, AN399_05715, AN400_17270, AN446_25935, AN447_15925, AN451_21855, AN453_22575, AN455_18155, AN456_19070, AN457_11175, AN458_15745, AN460_27980, AN462_17515, AOD73_08535, AOX61_ ...Gene: lecB, AN280_27645, AN399_05715, AN400_17270, AN446_25935, AN447_15925, AN451_21855, AN453_22575, AN455_18155, AN456_19070, AN457_11175, AN458_15745, AN460_27980, AN462_17515, AOD73_08535, AOX61_23230, AOX62_26425, APG03_22020, APG04_23970, APG05_03535, APG06_28020, APG07_27985, ATC05_02360, ERS445055_01627, PA8380_17510, PAERUG_E15_London_28_01_14_00983, PAERUG_P32_London_17_VIM_2_10_11_00423, PAMH19_1713, PAO1OR1608
Production host: Escherichia coli (E. coli) / References: UniProt: A0A069Q9V4, UniProt: Q9HYN5*PLUS
#2: Protein/peptide DLS-LYS-CYS-LYS-LEU-CYS-LEU-LYS-NH2


Mass: 1048.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / 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: obtained synthetically / Formula: C8H14O6
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 240 / 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: 2.09 Å3/Da / Density % sol: 41.27 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 0.2 M sodium acetate, 0.1 M Tris, 30% v/w PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.00004 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Oct 23, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00004 Å / Relative weight: 1
ReflectionResolution: 2.13→48.162 Å / Num. obs: 21998 / % possible obs: 98.9 % / Redundancy: 3.41 % / CC1/2: 0.988 / Rmerge(I) obs: 0.159 / Net I/σ(I): 7.66
Reflection shellResolution: 2.13→2.26 Å / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 2.86 / Num. unique all: 3410 / CC1/2: 0.788 / % possible all: 95.6

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4CE8

4ce8


Resolution: 2.13→48.162 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.16 / Phase error: 21.01
RfactorNum. reflection% reflection
Rfree0.225 2052 5 %
Rwork0.1793 --
obs0.1816 21975 94.24 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.13→48.162 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3355 0 60 240 3655
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043450
X-RAY DIFFRACTIONf_angle_d0.8324726
X-RAY DIFFRACTIONf_dihedral_angle_d9.6881976
X-RAY DIFFRACTIONf_chiral_restr0.059602
X-RAY DIFFRACTIONf_plane_restr0.003628
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1301-2.17960.2941080.24212190X-RAY DIFFRACTION79
2.1796-2.23410.24711320.23212527X-RAY DIFFRACTION92
2.2341-2.29450.24851400.2192608X-RAY DIFFRACTION94
2.2945-2.3620.29761380.22242619X-RAY DIFFRACTION95
2.362-2.43830.26261470.22562647X-RAY DIFFRACTION95
2.4383-2.52540.25791340.20792607X-RAY DIFFRACTION95
2.5254-2.62650.22451340.20542633X-RAY DIFFRACTION95
2.6265-2.74610.25821400.19722642X-RAY DIFFRACTION96
2.7461-2.89080.2381360.18782618X-RAY DIFFRACTION95
2.8908-3.07190.22051360.18512595X-RAY DIFFRACTION94
3.0719-3.3090.22851390.17112620X-RAY DIFFRACTION95
3.309-3.64190.21551410.13832645X-RAY DIFFRACTION97
3.6419-4.16870.18951440.14622696X-RAY DIFFRACTION97
4.1687-5.25110.19331420.1432684X-RAY DIFFRACTION97
5.2511-48.17470.18011410.16482664X-RAY DIFFRACTION97
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.18590.1607-0.26682.33990.68132.1020.05250.08390.1334-0.1131-0.0154-0.1528-0.2155-0.112-0.03380.12320.0309-0.00240.15210.00790.1231-17.1907-4.4349-3.8324
24.60651.3308-0.04170.63740.78882.50850.0860.33380.3105-0.51110.14510.1424-0.5505-0.1331-0.18840.2707-0.032-0.02060.13150.0320.145-17.5081-1.9553-11.8115
31.5050.0368-0.15292.18850.65121.4509-0.04260.02490.1355-0.11340.05790.1618-0.1456-0.1715-0.0060.17420.0082-0.01980.18720.01860.1203-17.7924-6.6865-7.7898
40.182-0.1226-0.12080.0737-0.08541.7839-0.0512-0.02420.0370.02360.0230.0407-0.0304-0.12690.01510.15070.01180.00040.1230.01170.1423-16.3054-11.13311.5032
55.0405-1.6503-1.35890.8794-0.23771.70160.02740.33580.07920.0378-0.0110.0362-0.1501-0.20580.01260.1564-0.0339-0.0210.1942-0.00550.1585-4.5807-2.5041-32.2527
62.20840.0570.00654.5694-0.99652.48640.061-0.32430.2320.1487-0.1298-0.1688-0.06350.1420.10770.1339-0.0177-0.00810.2231-0.04130.1398-7.2103-10.7822-21.8629
72.0467-1.1767-1.91366.9027-4.61557.83170.4132-0.5508-0.0470.256-0.2585-0.2087-0.54330.5617-0.15350.1493-0.0013-0.03050.335-0.09120.2521-5.5598-7.0256-17.0952
81.60540.8892-0.07511.9073-0.55731.3625-0.1634-0.07810.1112-0.07380.1762-0.0377-0.05250.1449-0.02030.17990.02040.01060.1873-0.0510.17-8.073-9.7825-22.431
94.723-0.70582.11471.66730.28421.80560.0821-0.4164-0.30720.02010.1793-0.0704-0.04480.0588-0.25780.148-0.05060.02030.2498-0.02060.1884-3.2907-13.5847-30.336
101.40410.62910.47120.4871-0.71563.88430.10380.2765-0.0956-0.1223-0.2023-0.14110.26120.55040.12360.1459-0.00470.0010.1624-0.03070.0863-7.2453-16.6227-31.457
110.88730.1632-0.19430.55420.38090.93870.07420.03-0.0621-0.0515-0.09690.1678-0.0495-0.1090.08390.15260.0012-0.00840.1312-0.01860.1484-13.965-7.2233-29.3498
121.37220.58490.45391.84670.62952.2960.06460.0261-0.01620.1607-0.06970.02160.224-0.0505-0.00230.10860.01450.0240.1310.00030.0843-22.4864-19.0646-33.239
133.9221-0.8458-0.11262.051-2.21252.67940.02080.0008-0.5802-0.1114-0.06360.89720.4065-0.4180.06960.1561-0.0654-0.02030.2710.0070.1851-30.1341-21.3338-32.6766
142.5419-2.3944-1.55762.00322.38044.87750.05490.0062-0.02320.4492-0.53741.04140.3479-0.56650.46770.1731-0.00430.05630.2708-0.01330.1925-31.0238-21.2176-27.8338
157.6168-0.554-2.99138.2574-2.42155.45680.3984-0.24990.42770.7517-0.2640.4876-0.37280.1092-0.13530.21650.02350.01710.1806-0.04690.1755-25.3873-3.5924-23.6366
162.3385-1.00270.44713.94011.03534.1543-0.1014-0.1371-0.2451-0.0622-0.00670.28350.4342-0.27130.09640.1309-0.03860.0230.1614-0.00040.1817-25.0414-22.4347-31.1286
178.03930.5778-2.84670.31461.18678.11890.1358-0.07450.29140.3877-0.00940.8249-0.7507-0.9513-0.11410.24880.05160.1260.2084-0.00240.2967-36.9896-9.1031-34.2978
180.81090.3103-0.39440.1390.02611.2456-0.0070.1884-0.0672-0.08050.0305-0.0321-0.0207-0.0333-0.05550.1448-0.02030.0060.1244-0.030.1324-18.6372-14.11-35.7215
191.74491.2647-0.37112.7594-1.14751.2166-0.04560.0047-0.0451-0.00550.0126-0.00170.05530.0270.0380.12280.02060.02740.1482-0.01440.1122-4.6197-20.57341.6539
202.6404-0.42130.57261.0321.66963.3436-0.1086-0.0385-0.433-0.11170.1893-0.66720.3136-0.1515-0.06590.15680.0188-0.00360.19190.00520.19022.1865-24.62360.6135
210.87791.122-0.36164.58980.14361.7134-0.0891-0.0395-0.0791-0.44520.019-0.36790.06260.05820.07310.1333-0.00130.01990.17970.02560.1259-0.1043-17.8042-5.7044
221.42910.2285-0.33740.5311-0.21350.73030.0144-0.1591-0.10420.0491-0.033-0.06440.03850.12550.01890.11980.0150.01160.1068-0.00280.1144-4.5589-17.50914.661
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 34 )
2X-RAY DIFFRACTION2chain 'A' and (resid 35 through 42 )
3X-RAY DIFFRACTION3chain 'A' and (resid 43 through 74 )
4X-RAY DIFFRACTION4chain 'A' and (resid 75 through 114 )
5X-RAY DIFFRACTION5chain 'B' and (resid 1 through 12 )
6X-RAY DIFFRACTION6chain 'B' and (resid 13 through 34 )
7X-RAY DIFFRACTION7chain 'B' and (resid 35 through 42 )
8X-RAY DIFFRACTION8chain 'B' and (resid 43 through 69 )
9X-RAY DIFFRACTION9chain 'B' and (resid 70 through 83 )
10X-RAY DIFFRACTION10chain 'B' and (resid 84 through 104 )
11X-RAY DIFFRACTION11chain 'B' and (resid 105 through 114 )
12X-RAY DIFFRACTION12chain 'C' and (resid 1 through 25 )
13X-RAY DIFFRACTION13chain 'C' and (resid 26 through 34 )
14X-RAY DIFFRACTION14chain 'C' and (resid 35 through 42 )
15X-RAY DIFFRACTION15chain 'C' and (resid 43 through 47 )
16X-RAY DIFFRACTION16chain 'C' and (resid 48 through 68 )
17X-RAY DIFFRACTION17chain 'C' and (resid 69 through 74 )
18X-RAY DIFFRACTION18chain 'C' and (resid 75 through 114 )
19X-RAY DIFFRACTION19chain 'D' and (resid 1 through 25 )
20X-RAY DIFFRACTION20chain 'D' and (resid 26 through 34 )
21X-RAY DIFFRACTION21chain 'D' and (resid 35 through 56 )
22X-RAY DIFFRACTION22chain 'D' and (resid 57 through 114 )

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Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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