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- PDB-6y0u: Fucosylated Bicyclic peptide bp71 bound to the fucose binding lec... -

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Basic information

Entry
Database: PDB / ID: 6y0u
TitleFucosylated Bicyclic peptide bp71 bound to the fucose binding lectin LecB PA-IIL from Pseudomonas aeruginosa at 1.5 Angstrom resolution
Components
  • Fucose-binding lectin
  • bp71
KeywordsANTIBIOTIC / Antimicrobial / Bicyclic / Lectin
Function / homology
Function and homology information


single-species biofilm formation / carbohydrate binding / metal ion binding
Similarity search - Function
Lectin, sugar-binding / Calcium-mediated lectin / Calcium-mediated lectin superfamily / Fucose-binding lectin II (PA-IIL)
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 / molecular replacement / Resolution: 1.489 Å
AuthorsBaeriswyl, S. / Stocker, A. / Reymond, J.-L.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science Foundation Switzerland
Citation
Journal: Rsc Chem Biol / Year: 2021
Title: A mixed chirality alpha-helix in a stapled bicyclic and a linear antimicrobial peptide revealed by X-ray crystallography.
Authors: Baeriswyl, S. / Personne, H. / Di Bonaventura, I. / Kohler, T. / van Delden, C. / Stocker, A. / Javor, S. / Reymond, J.L.
#1: Journal: Rsc Chem Biol / Year: 2021
Title: A mixed chirality alpha-helix in a stapled bicyclic and a linear antimicrobial peptide revealed by X-ray crystallography.
Authors: Baeriswyl, S. / Personne, H. / Di Bonaventura, I. / Kohler, T. / van Delden, C. / Stocker, A. / Javor, S. / Reymond, J.L.
#2: Journal: Rsc Chem Biol / Year: 2021
Title: A mixed chirality alpha-helix in a stapled bicyclic and a linear antimicrobial peptide revealed by X-ray crystallography.
Authors: Baeriswyl, S. / Personne, H. / Di Bonaventura, I. / Kohler, T. / van Delden, C. / Stocker, A. / Javor, S. / Reymond, J.L.
#3: Journal: Chemrxiv / Year: 2021
Title: Mixed chirality alpha-helix in a stapled bicyclic and a linear antimicrobial peptide revealed by X-ray crystallography
Authors: Personne, H. / Baeriswyl, S. / Di Bonaventura, I. / Kohler, T. / van Delden, C. / Stocker, A. / Javor, S. / Reymond, J.-L.
History
DepositionFeb 10, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 24, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2021Group: Database references / Structure summary
Category: citation / citation_author ...citation / citation_author / entity / struct
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _entity.details / _entity.pdbx_description / _struct.pdbx_descriptor / _struct.title
Revision 1.2Feb 2, 2022Group: Database references / Category: citation / citation_author / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.0Feb 1, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / citation / entity / entity_poly / entity_poly_seq / pdbx_entity_nonpoly / pdbx_entity_src_syn / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / pdbx_validate_symm_contact / struct_asym / struct_conf / struct_conn / struct_ref_seq
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.group_PDB / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.label_seq_id / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.pdbx_label_seq_id / _atom_site_anisotrop.type_symbol / _citation.journal_id_ISSN / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_entity_src_syn.pdbx_end_seq_num / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_special_symmetry.label_asym_id / _pdbx_validate_symm_contact.auth_seq_id_1 / _struct_conf.beg_auth_seq_id / _struct_conf.beg_label_seq_id / _struct_conf.end_auth_seq_id / _struct_conf.end_label_seq_id / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_ref_seq.seq_align_end
Revision 2.1Feb 7, 2024Group: Data collection / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_conn
Item: _struct_conn.pdbx_leaving_atom_flag
Revision 2.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fucose-binding lectin
E: bp71
B: Fucose-binding lectin
F: bp71
C: Fucose-binding lectin
D: Fucose-binding lectin
H: bp71
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,43319
Polymers52,2887
Non-polymers1,14512
Water8,719484
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10460 Å2
ΔGint-132 kcal/mol
Surface area18370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)122.821, 56.600, 70.452
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11B-501-

HOH

21C-462-

HOH

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Components

#1: Protein
Fucose-binding lectin / Fucose-binding lectin II (PA-IIL) / Fucose-binding lectin PA-IIL


Mass: 11865.905 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: Fucose binding Lectin LecB PA-IIL from Pseudomonas aeruginosa
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria)
Gene: lecB, C0044_25260, CAZ10_21840, DT376_00595, DY979_15445, ECC04_10105, EFK27_13700, EGV95_09240, EGY23_15550, IPC669_23070, PA5486_01888, PAERUG_E15_London_28_01_14_00983, PAMH19_1713, RW109_RW109_02453
Production host: Escherichia coli BL21 (bacteria) / References: UniProt: A0A069Q9V4, UniProt: Q9HYN5*PLUS
#2: Protein/peptide bp71


Mass: 1608.153 Da / Num. of mol.: 3 / Source method: obtained synthetically / Details: Fucosylated Bicyclic peptide bp71 / 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: isolated from a genetically manipulated source
Formula: C8H14O6
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 484 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.37 Å3/Da / Density % sol: 48.01 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 1.5 M Ammonium sulfate, 0.1 M Tris pH 8.5, 12% v/v Glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Sep 22, 2017
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.489→46.293 Å / Num. obs: 144479 / % possible obs: 92.9 % / Redundancy: 1.74 % / Biso Wilson estimate: 23.591 Å2 / CC1/2: 0.997 / Rrim(I) all: 0.075 / Χ2: 0.93 / Net I/σ(I): 6.16
Reflection shellResolution: 1.489→1.496 Å / Redundancy: 1.59 % / Mean I/σ(I) obs: 1.31 / Num. unique obs: 22185 / CC1/2: 0.578 / Rrim(I) all: 0.844 / Χ2: 0.72 / % possible all: 88.3

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.84 Å46.29 Å
Translation2.84 Å46.29 Å

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHASER2.8.0phasing
PHENIXv1.11.1-2575refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1OXC

1oxc


Resolution: 1.489→46.293 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.24 / Phase error: 19.89
RfactorNum. reflection% reflection
Rfree0.1919 7252 5.02 %
Rwork0.1682 --
obs0.1694 144416 92.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 93.56 Å2 / Biso mean: 23.7915 Å2 / Biso min: 10.68 Å2
Refinement stepCycle: final / Resolution: 1.489→46.293 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3558 0 60 484 4102
Biso mean--18.05 35.49 -
Num. residues----498
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063659
X-RAY DIFFRACTIONf_angle_d0.8225000
X-RAY DIFFRACTIONf_chiral_restr0.09634
X-RAY DIFFRACTIONf_plane_restr0.004661
X-RAY DIFFRACTIONf_dihedral_angle_d8.6051192
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.489-1.50570.33232190.3291398381
1.5057-1.52350.34352290.3069422687
1.5235-1.5420.30942320.2877446791
1.542-1.56160.29122340.2693451791
1.5616-1.58210.26792370.2615456693
1.5821-1.60380.27812430.2571459594
1.6038-1.62670.31082390.2531458593
1.6267-1.6510.25732360.2387450092
1.651-1.67680.26032510.2246468096
1.6768-1.70430.24162550.2239480597
1.7043-1.73370.25412440.2164475696
1.7337-1.76520.2642440.2012469096
1.7652-1.79910.19962520.1926470896
1.7991-1.83590.21312540.1765472796
1.8359-1.87580.18772480.1693464495
1.8758-1.91940.18292480.155467695
1.9194-1.96740.18162520.1536467895
1.9674-2.02060.19352530.1531462394
2.0206-2.08010.19122380.1591461994
2.0801-2.14720.17872430.1546449891
2.1472-2.2240.17532370.1438442291
2.224-2.3130.17812240.1491440889
2.313-2.41830.16572460.1483462994
2.4183-2.54570.18322440.1545463795
2.5457-2.70520.16742410.1483469795
2.7052-2.91410.1512490.1446459494
2.9141-3.20730.15122460.1399466095
3.2073-3.67120.15722410.1293456093
3.6712-4.62460.16162290.1442440789
4.6246-46.2930.2162440.1861460793
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)
11.9153-0.0235-1.60171.5042-0.33042.4684-0.01950.12850.0858-0.0882-0.0272-0.00130.0024-0.10950.03820.18760.0063-0.00670.16470.00310.1501-28.076420.2242-30.7557
23.5164.2073-1.77198.1552-4.27022.5589-0.0211-0.1113-0.1614-0.1975-0.1776-0.21560.17130.07510.22140.14320.0105-0.00170.1295-0.0210.1199-27.2184.6087-26.5519
3-0.0054-0.0242-0.01519.0376-6.6435.19480.01270.07130.0891-0.4570.08110.21990.2112-0.2295-0.18320.2052-0.0108-0.01610.15470.00310.1435-33.888510.4471-33.3507
41.0401-0.49440.06392.09390.06610.58020.0726-0.01910.036-0.06-0.0446-0.03270.18570.0583-0.08010.1618-0.0146-0.00220.1211-0.00270.1316-30.88311.9717-28.6204
52.4564.7038-3.71199.7028-7.36285.6404-0.06060.09750.0011-0.32740.07280.02240.1996-0.0364-0.03070.2013-0.00070.00980.172-0.01090.1435-24.11275.1679-32.8036
61.19961.8697-2.43794.7481-3.89864.5655-0.04550.12740.1449-0.16650.15070.284-0.005-0.1621-0.10840.1903-0.0214-0.02930.17280.00850.1543-32.457614.5931-32.6193
73.51022.94534.34532.5263.66375.38820.4504-0.1462-1.04310.0655-0.23050.63050.4147-0.3861-0.00190.20410.0017-0.06090.1953-0.02020.3366-42.74535.1542-24.7069
84.90463.3749-0.03553.41610.11130.0119-0.0247-0.0861-0.0454-0.0676-0.0129-0.0395-0.0070.04120.04380.1553-0.0027-0.00630.15170.01190.1137-23.881316.7968-22.6312
90.54380.42550.2741.4740.01160.2840.0063-0.11280.08810.038-0.02340.1030.07330.01830.00530.1599-0.0022-0.00140.1507-0.00420.1341-28.38659.1714-21.5373
100.77690.0741-0.23950.78580.27482.07220.0449-0.0246-0.06230.018-0.011-0.13460.20610.0965-0.01670.1770.0237-0.00730.15780.01090.1867-11.99773.6732-18.0212
116.09412.1514-4.85730.7783-1.73313.8463-0.2149-0.354-0.2216-0.035-0.1104-0.22760.25010.67830.34440.17950.03880.00450.22460.01990.2227-6.17996.7791-15.7396
122.16621.65781.82546.08865.90235.83730.50240.3118-0.0923-0.8838-0.0643-1.2463-0.11780.4495-0.29330.21830.05480.0550.2138-0.03880.34781.78717.9689-23.7663
130.1546-0.27610.06251.37130.53780.62030.02220.01470.0483-0.03850.0018-0.13210.02610.0674-0.03830.12840.0101-0.00340.14140.00660.1399-15.705512.5313-19.4394
141.26150.1470.70040.7943-0.09242.89370.01660.04290.1159-0.0244-0.0339-0.0182-0.18620.09530.03430.1622-0.02070.01320.13230.00140.1685-13.77635.7234-17.2077
155.8334-1.30240.88836.99663.87042.60380.22810.15290.126-0.10340.1524-0.0628-1.2640.0748-0.20470.188-0.0604-0.00790.16140.00010.199-10.764543.2742-15.642
164.71041.88334.97420.7581.80757.37830.6138-0.92610.4030.8268-0.46940.36030.2144-0.4598-0.19970.2396-0.04380.00910.1957-0.02490.1923-14.472936.0251.4198
171.0415-0.46111.07630.98050.28654.25620.00180.12710.204-0.0712-0.0276-0.0849-0.12540.15840.01470.1737-0.0470.01450.12690.02410.1814-14.706538.642-18.6653
188.36464.4559-3.06093.618-3.95246.00260.1511-0.4225-0.0650.3735-0.02930.0255-0.26890.2532-0.05530.1671-0.01980.0070.1682-0.00970.1786-0.601835.0199-7.9183
190.06360.17220.02140.40630.230.4627-0.00370.0065-0.0065-0.0378-0.0046-0.0473-0.05040.02260.02060.1344-0.01480.00450.13810.00440.1332-17.110628.5068-13.9126
206.08730.43844.73151.85090.96964.7693-0.009-0.1211-0.19980.0442-0.00350.05380.0899-0.19470.00030.1679-0.01350.04370.14220.00590.135-28.835419.2109-3.3705
211.5328-2.4711.33667.1931-5.29114.98270.03850.0409-0.0110.14350.0550.2721-0.0748-0.1037-0.08450.17260.00780.01080.09-0.04420.0988-32.419832.0317-4.9698
222.4691-1.97812.4028.231-3.59332.90950.0901-0.0450.15630.6460.15780.48-0.4186-0.244-0.14570.20150.00960.02180.1512-0.00180.1646-35.187932.80240.5316
238.6-2.7273-1.69484.40471.45342.9714-0.00670.21250.3168-0.0231-0.0065-0.0237-0.31490.0034-0.01030.25180.0112-0.00760.15720.00330.1775-31.400942.6612-14.6814
245.4728-5.58825.86975.7001-5.98886.1993-0.1048-0.06930.01470.5990.08070.1461-0.5479-0.04490.12290.23660.0110.01260.1383-0.02490.1444-26.706734.0433-0.4051
258.5297-6.34968.74045.0007-7.01179.8290.0072-0.2383-0.08430.20080.1940.2812-0.0979-0.3443-0.39430.16950.00820.03230.15670.00360.1725-33.295823.1868-1.0684
263.4196-3.5339-3.85873.69924.08424.6327-0.03880.42550.40580.3968-0.14291.6334-0.3791-0.92270.25170.23420.0590.04850.2129-0.0170.4027-44.696232.8307-10.6102
274.6282-2.38040.59442.8789-0.20890.14820.01510.0881-0.02330.0098-0.04480.04-0.0070.00290.02890.1375-0.00740.01230.14650.00360.1182-24.615123.0703-11.2572
281.6447-0.86670.40331.2677-0.25051.08410.02640.0564-0.1883-0.08190.02470.1679-0.0895-0.0418-0.10540.1538-0.00190.00120.1437-0.00380.1706-30.099830.1841-12.7503
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 12 )A1 - 12
2X-RAY DIFFRACTION2chain 'A' and (resid 13 through 25 )A13 - 25
3X-RAY DIFFRACTION3chain 'A' and (resid 26 through 34 )A26 - 34
4X-RAY DIFFRACTION4chain 'A' and (resid 35 through 47 )A35 - 47
5X-RAY DIFFRACTION5chain 'A' and (resid 48 through 56 )A48 - 56
6X-RAY DIFFRACTION6chain 'A' and (resid 57 through 69 )A57 - 69
7X-RAY DIFFRACTION7chain 'A' and (resid 70 through 74 )A70 - 74
8X-RAY DIFFRACTION8chain 'A' and (resid 75 through 95 )A75 - 95
9X-RAY DIFFRACTION9chain 'A' and (resid 96 through 114 )A96 - 114
10X-RAY DIFFRACTION10chain 'B' and (resid 1 through 61 )B1 - 61
11X-RAY DIFFRACTION11chain 'B' and (resid 62 through 69 )B62 - 69
12X-RAY DIFFRACTION12chain 'B' and (resid 70 through 74 )B70 - 74
13X-RAY DIFFRACTION13chain 'B' and (resid 75 through 114 )B75 - 114
14X-RAY DIFFRACTION14chain 'C' and (resid 1 through 34 )C1 - 34
15X-RAY DIFFRACTION15chain 'C' and (resid 35 through 42 )C35 - 42
16X-RAY DIFFRACTION16chain 'C' and (resid 43 through 47 )C43 - 47
17X-RAY DIFFRACTION17chain 'C' and (resid 48 through 68 )C48 - 68
18X-RAY DIFFRACTION18chain 'C' and (resid 69 through 74 )C69 - 74
19X-RAY DIFFRACTION19chain 'C' and (resid 75 through 114 )C75 - 114
20X-RAY DIFFRACTION20chain 'D' and (resid 1 through 12 )D1 - 12
21X-RAY DIFFRACTION21chain 'D' and (resid 13 through 34 )D13 - 34
22X-RAY DIFFRACTION22chain 'D' and (resid 35 through 42 )D35 - 42
23X-RAY DIFFRACTION23chain 'D' and (resid 43 through 48 )D43 - 48
24X-RAY DIFFRACTION24chain 'D' and (resid 49 through 56 )D49 - 56
25X-RAY DIFFRACTION25chain 'D' and (resid 57 through 68 )D57 - 68
26X-RAY DIFFRACTION26chain 'D' and (resid 69 through 74 )D69 - 74
27X-RAY DIFFRACTION27chain 'D' and (resid 75 through 95 )D75 - 95
28X-RAY DIFFRACTION28chain 'D' and (resid 96 through 114 )D96 - 114

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