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- PDB-5i8x: Bicyclic antimibrocial peptides -

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Basic information

Entry
Database: PDB / ID: 5i8x
TitleBicyclic antimibrocial peptides
Components
  • DLS-LYS-CYS-LYS-LEU-CYS-LYS-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 / 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: 1.89 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 / pdbx_validate_close_contact / 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 / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _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-LYS-LYS-NH2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,13317
Polymers47,9875
Non-polymers1,14512
Water5,909328
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8910 Å2
ΔGint-111 kcal/mol
Surface area16540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.424, 79.202, 52.627
Angle α, β, γ (deg.)90.00, 94.52, 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-LYS-LYS-NH2


Mass: 1048.409 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: obtained synthetically / Formula: C8H14O6
#4: Chemical
ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 328 / 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: 2.1 Å3/Da / Density % sol: 41.38 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 0.2 M Ammonium Acetate 0.1 M Sodium Acetate 30 w/v PEG4000

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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: 1.89→48.273 Å / Num. obs: 31514 / % possible obs: 98.9 % / Redundancy: 3.33 % / CC1/2: 0.983 / Rmerge(I) obs: 0.184 / Net I/σ(I): 6.13
Reflection shellResolution: 1.89→2 Å / Rmerge(I) obs: 0.604 / Mean I/σ(I) obs: 2.3 / Num. unique all: 4900 / CC1/2: 0.727 / % 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: 1.89→48.273 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 0.91 / Phase error: 22.33
RfactorNum. reflection% reflection
Rfree0.2228 2947 4.98 %
Rwork0.1828 --
obs0.1848 31491 94.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.89→48.273 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3348 0 60 328 3736
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063466
X-RAY DIFFRACTIONf_angle_d0.8844755
X-RAY DIFFRACTIONf_dihedral_angle_d9.9291987
X-RAY DIFFRACTIONf_chiral_restr0.064607
X-RAY DIFFRACTIONf_plane_restr0.004632
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.889-1.91990.32071100.2822123X-RAY DIFFRACTION75
1.9199-1.9530.30721300.25662659X-RAY DIFFRACTION93
1.953-1.98850.25841370.23792639X-RAY DIFFRACTION93
1.9885-2.02680.2781410.23672689X-RAY DIFFRACTION94
2.0268-2.06820.30181400.22922635X-RAY DIFFRACTION94
2.0682-2.11310.26871430.22492703X-RAY DIFFRACTION94
2.1131-2.16230.22921410.21522660X-RAY DIFFRACTION95
2.1623-2.21640.25091420.21512712X-RAY DIFFRACTION95
2.2164-2.27630.26551420.20532700X-RAY DIFFRACTION95
2.2763-2.34330.27581360.20392618X-RAY DIFFRACTION95
2.3433-2.41890.22761400.19882700X-RAY DIFFRACTION94
2.4189-2.50530.23161410.19682665X-RAY DIFFRACTION94
2.5053-2.60570.2151380.19952621X-RAY DIFFRACTION94
2.6057-2.72420.25581450.18452771X-RAY DIFFRACTION97
2.7242-2.86780.2221500.17512800X-RAY DIFFRACTION99
2.8678-3.04750.20951490.16152797X-RAY DIFFRACTION99
3.0475-3.28270.17511500.15692789X-RAY DIFFRACTION99
3.2827-3.6130.20531440.14362742X-RAY DIFFRACTION97
3.613-4.13560.20681390.14082751X-RAY DIFFRACTION97
4.1356-5.20940.1491380.14082677X-RAY DIFFRACTION95
5.2094-48.28920.18861510.16042807X-RAY DIFFRACTION99
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)
11.9596-0.7016-0.25361.9380.77642.62040.050.0364-0.05820.0776-0.0240.14150.3106-0.2349-0.03040.0992-0.0264-0.00450.1172-0.00660.0981-2.59483.4831-6.9005
27.35970.2654-0.20932.0137.23394.70540.17690.12050.1799-0.2747-0.52840.58250.1271-0.69760.39760.2442-0.0013-0.00180.1682-0.00070.1134-8.99031.9181-1.6507
30.7957-1.07830.11023.89340.92423.20060.0322-0.0538-0.1144-0.07990.04460.12910.2103-0.0881-0.03430.0681-0.03610.01430.13180.00550.1373-3.46475.1473-3.4143
46.63843.945-4.62517.1237-3.50059.9312-0.0564-0.0780.59260.1105-0.02190.9731-0.4045-0.47270.08220.1509-0.0189-0.01860.207-0.00170.2345-15.204313.8814-8.622
50.959-0.0491-0.45960.11490.46631.2005-0.04230.11330.0384-0.0470.0227-0.01030.06-0.08230.01140.0903-0.0159-0.00730.09760.00320.11643.28579.2132-9.5697
67.83913.62531.64812.59491.07552.11310.0909-0.2528-0.0018-0.0683-0.09-0.2381-0.0827-0.056-0.02140.13360.0243-0.01670.0706-0.00460.14278.566423.2445-22.3824
71.7470.47242.12753.12082.40354.60440.04250.1251-0.15-0.21250.1865-0.4098-0.0468-0.0445-0.18940.0679-0.00780.02340.10250.01680.096711.684212.4223-34.1647
82.93811.87491.02048.94172.91151.9332-0.20780.33240.3155-0.3480.35310.2917-0.4859-0.111-0.13150.20970.010.02960.16380.04120.12715.828921.769-33.9079
93.8364-0.8549-1.83124.01353.60756.26670.21250.17750.4183-0.8776-0.40360.0493-0.7017-0.43010.1760.19890.0413-0.04390.12970.03580.14268.573721.2381-37.9714
102.64352.43191.39353.53663.16833.0617-0.06320.0340.1761-0.5112-0.01070.0711-0.21140.2031-0.00320.1006-0.0103-0.00930.10910.01190.094313.897212.0075-36.6545
111.00440.4141-0.25544.45191.53813.3149-0.34290.11810.53770.07740.03320.6757-0.4711-0.43110.36150.12970.0358-0.02890.13570.00240.18876.07322.9741-29.3904
123.89130.9982.05021.62671.31074.1511-0.10580.0214-0.0811-0.0570.109-0.0104-0.1508-0.1712-00.08730.00110.01740.0840.01360.1048.871213.7666-23.7671
131.5405-2.21982.95565.9826-1.61168.1625-0.1785-0.2591-0.0619-0.01620.25540.26430.1497-0.6055-0.0460.11150.00040.01770.14520.00720.0986-0.11233.3227-31.0824
141.4740.6217-0.14781.28680.15560.05950.02780.11990.0578-0.1642-0.0709-0.10590.02280.10540.0580.14480.0049-0.020.09460.02740.08316.45816.8888-26.2566
152.45911.73550.8532.63192.97474.36620.0165-0.0015-0.15290.08410.0903-0.11020.31430.1295-0.07690.12730.01640.00290.10880.04210.117118.5313-3.2641-19.2386
163.6232.584-0.44795.6984-0.25590.8128-0.08510.0477-0.0911-0.09330.0202-0.10510.12570.16130.07010.10930.01360.02010.10820.00890.050126.09734.3645-27.886
176.81844.342-1.08676.3809-3.45533.2779-0.09080.0787-0.21750.07470.16340.06240.515-0.0397-0.11870.2187-0.00730.02050.0782-0.00560.104229.2366-0.6999-30.454
184.1611-2.0462-2.39457.2722.81583.85630.4449-0.06540.9625-0.44240.2226-0.4712-0.45790.076-0.55120.1299-0.01330.05670.19410.03770.187228.559218.2461-31.5783
192.41212.586-0.00817.1119-0.06672.64180.00640.0348-0.0904-0.07190.0337-0.38280.09850.239-0.04690.08280.00090.01010.13150.00640.088521.90532.853-33.3539
201.83330.9261-0.45824.2887-0.34212.19980.081-0.2479-0.28580.1-0.08-0.52480.25090.1408-0.04150.15140.0291-0.00540.118-0.04870.169624.1382-3.8089-22.3352
216.19791.4706-0.60220.4241-0.18620.7738-0.0003-0.24930.0474-0.0428-0.0301-0.00960.00730.03080.05790.12640.0155-0.00820.08970.01050.111419.84216.493-20.0085
224.02781.0966-0.88334.7962-2.47961.3203-0.1636-0.1139-0.04690.55530.0163-0.3032-0.05470.01520.14690.16630.0161-0.01090.1109-0.02450.161430.426616.7729-18.5461
236.20994.18271.37983.63310.35530.69850.0466-0.01940.04570.02240.03290.0292-0.0735-0.0222-0.08620.10630.00280.01670.0611-0.01420.104115.41513.4784-27.2102
240.44130.3425-0.84513.5833-0.6941.60310.0547-0.01710.05380.0862-0.01310.1455-0.07470.0354-0.04090.0671-0.0134-0.04510.1354-0.02870.108214.279214.7354-0.8883
251.3897-1.2209-0.07452.3548-2.37314.6090.1837-0.33590.30780.2686-0.4113-0.2811-0.26980.27740.28010.1137-0.0119-0.00280.2226-0.03010.181518.068216.46526.9358
262.11371.2487-0.64664.9188-1.73431.5339-0.0083-0.12370.03030.1597-0.0253-0.1199-0.10650.12070.05570.1010.0095-0.01090.1225-0.02710.076313.925213.44443.8208
270.37530.152-0.62641.6362-0.55091.59820.002-0.20980.16030.00010.057-0.1562-0.00730.0963-0.03180.0849-0.0175-0.01080.1047-0.02550.076414.648911.528-6.5543
280.46340.362-0.5060.3262-0.20491.0345-0.02190.0553-0.1406-0.0848-0.01550.01260.01820.12820.06880.11380.003-0.02230.1551-0.02750.124114.16227.1535-2.0221
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 69 )
4X-RAY DIFFRACTION4chain 'A' and (resid 70 through 74 )
5X-RAY DIFFRACTION5chain 'A' and (resid 75 through 114 )
6X-RAY DIFFRACTION6chain 'B' and (resid 1 through 12 )
7X-RAY DIFFRACTION7chain 'B' and (resid 13 through 25 )
8X-RAY DIFFRACTION8chain 'B' and (resid 26 through 34 )
9X-RAY DIFFRACTION9chain 'B' and (resid 35 through 42 )
10X-RAY DIFFRACTION10chain 'B' and (resid 43 through 56 )
11X-RAY DIFFRACTION11chain 'B' and (resid 57 through 69 )
12X-RAY DIFFRACTION12chain 'B' and (resid 70 through 95 )
13X-RAY DIFFRACTION13chain 'B' and (resid 96 through 104 )
14X-RAY DIFFRACTION14chain 'B' and (resid 105 through 114 )
15X-RAY DIFFRACTION15chain 'C' and (resid 1 through 12 )
16X-RAY DIFFRACTION16chain 'C' and (resid 13 through 34 )
17X-RAY DIFFRACTION17chain 'C' and (resid 35 through 42 )
18X-RAY DIFFRACTION18chain 'C' and (resid 43 through 47 )
19X-RAY DIFFRACTION19chain 'C' and (resid 48 through 56 )
20X-RAY DIFFRACTION20chain 'C' and (resid 57 through 68 )
21X-RAY DIFFRACTION21chain 'C' and (resid 69 through 95 )
22X-RAY DIFFRACTION22chain 'C' and (resid 96 through 104 )
23X-RAY DIFFRACTION23chain 'C' and (resid 105 through 114 )
24X-RAY DIFFRACTION24chain 'D' and (resid 1 through 25 )
25X-RAY DIFFRACTION25chain 'D' and (resid 26 through 42 )
26X-RAY DIFFRACTION26chain 'D' and (resid 43 through 69 )
27X-RAY DIFFRACTION27chain 'D' and (resid 70 through 95 )
28X-RAY DIFFRACTION28chain 'D' and (resid 96 through 114 )

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