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- PDB-6q8h: Structure of Fucosylated D-antimicrobial peptide SB10 in complex ... -

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Basic information

Entry
Database: PDB / ID: 6q8h
TitleStructure of Fucosylated D-antimicrobial peptide SB10 in complex with the Fucose-binding lectin PA-IIL at 1.707 Angstrom resolution
Components
  • Fucose-binding lectin
  • SB10
KeywordsANTIBIOTIC / Antimicrobial / Lectin / Complex
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
AMINO GROUP / Chem-ZDC / polypeptide(D) / polypeptide(D) (> 10) / 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: 1.707 Å
AuthorsBaeriswyl, S. / Stocker, A. / Reymond, J.L.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science Foundation Switzerland
CitationJournal: Acs Chem.Biol. / Year: 2019
Title: X-ray Crystal Structures of Short Antimicrobial Peptides as Pseudomonas aeruginosa Lectin B Complexes.
Authors: Baeriswyl, S. / Gan, B.H. / Siriwardena, T.N. / Visini, R. / Robadey, M. / Javor, S. / Stocker, A. / Darbre, T. / Reymond, J.L.
History
DepositionDec 14, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 20, 2019Provider: repository / Type: Initial release
Revision 1.1May 1, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
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_comp_id ..._chem_comp.type / _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.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.ptnr2_symmetry / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.0Dec 7, 2022Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / database_2 / 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_unobs_or_zero_occ_residues / pdbx_validate_close_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.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 / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_special_symmetry.label_asym_id / _struct_conf.beg_auth_comp_id / _struct_conf.beg_auth_seq_id / _struct_conf.beg_label_comp_id / _struct_conf.beg_label_seq_id / _struct_conf.end_label_seq_id / _struct_conf.pdbx_PDB_helix_length / _struct_ref_seq.db_align_beg / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.seq_align_end
Revision 2.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fucose-binding lectin
B: SB10
C: SB10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,3499
Polymers14,8253
Non-polymers5256
Water3,189177
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1200 Å2
ΔGint-16 kcal/mol
Surface area8630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)131.522, 131.522, 49.920
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number180
Space group name H-MP6222
Components on special symmetry positions
IDModelComponents
11A-409-

HOH

21A-525-

HOH

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Components

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Protein / Polypeptide(D) / Sugars , 3 types, 5 molecules ABC

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


Mass: 11734.707 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Fucose-binding lectin PA-IIL LecB / Source: (gene. exp.) Pseudomonas aeruginosa (bacteria)
Gene: lecB, C0043_24310, C0044_25260, C0046_23510, CAZ10_21840, CW299_25270, DI492_13230, DT376_00595, PAERUG_E15_London_28_01_14_00983, PAMH19_1713, RW109_RW109_02453
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A069Q9V4, UniProt: Q9HYN5*PLUS
#2: Polypeptide(D) SB10


Mass: 1545.013 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: Fucosylated D-antimicrobial peptide SB10. Full sequence: (FUD)(DLE)(DLE)(DLY)(DAL)(DLE)(DLY)(DLY)(DLE)(DAL)(DLY)(DLY)(DTY)(DLY)
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.: 2 / Source method: obtained synthetically / Formula: C8H14O6

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Non-polymers , 3 types, 181 molecules

#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: Ca
#5: Chemical ChemComp-NH2 / AMINO GROUP


Mass: 16.023 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: NH2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 177 / 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: 4.11 Å3/Da / Density % sol: 70.1 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 15% v/v Tacsimate pH 7.0, 0.1 M HEPES pH 7.0, 2% w/v Polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.00004 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Oct 23, 2015
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00004 Å / Relative weight: 1
ReflectionResolution: 1.707→45.722 Å / Num. obs: 27907 / % possible obs: 99.4 % / Redundancy: 13.1 % / Rpim(I) all: 0.025 / Rrim(I) all: 0.09 / Rsym value: 0.086 / Net I/av σ(I): 8.3 / Net I/σ(I): 20.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsRpim(I) allRrim(I) allRsym value% possible all
1.71-1.813.32.2220.439260.622.3092.22297.8
1.8-1.9113.51.1870.737690.3291.2321.18799.2
1.91-2.0413.30.5851.335670.1650.6090.58599.3
2.04-2.212.30.3292.433410.0970.3430.32999.6
2.2-2.41130.2063.830980.0590.2140.20699.7
2.41-2.713.80.1395.628190.0380.1440.13999.8
2.7-3.1213.40.07310.425230.020.0760.07399.9
3.12-3.8212.50.03818.621460.0110.0390.038100
3.82-5.4120.02626.117040.0080.0270.026100
5.4-45.72212.50.02325.910140.0070.0240.02399.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHENIXrefinement
XDSdata reduction
SCALA3.3.22data scaling
PHASERphasing
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1OXC

1oxc


Resolution: 1.707→45.722 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 20.16
RfactorNum. reflection% reflection
Rfree0.1888 2607 5 %
Rwork0.1675 --
obs0.1686 27906 99.24 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 119.56 Å2 / Biso mean: 40.2667 Å2 / Biso min: 20.44 Å2
Refinement stepCycle: final / Resolution: 1.707→45.722 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1015 0 20 177 1212
Biso mean--57.55 46.88 -
Num. residues----140
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071071
X-RAY DIFFRACTIONf_angle_d0.8751457
X-RAY DIFFRACTIONf_chiral_restr0.067187
X-RAY DIFFRACTIONf_plane_restr0.005185
X-RAY DIFFRACTIONf_dihedral_angle_d8.125570
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 19

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7071-1.73810.33261340.33942534266896
1.7381-1.77150.36941370.33142545268298
1.7715-1.80770.36071350.29992622275799
1.8077-1.8470.28531420.27692568271098
1.847-1.890.26091370.246925852722100
1.89-1.93720.26781330.21392605273899
1.9372-1.98960.24381370.20532646278399
1.9896-2.04810.23141350.19182576271199
2.0481-2.11430.21141360.19692602273899
2.1143-2.18980.20911380.1832630276899
2.1898-2.27750.19291370.166626172754100
2.2775-2.38110.16681420.153526222764100
2.3811-2.50670.18911390.166726102749100
2.5067-2.66370.18581340.162226322766100
2.6637-2.86930.18931400.158726122752100
2.8693-3.1580.15841380.169626192757100
3.158-3.61490.15341340.15226422776100
3.6149-4.55370.18061320.135426312763100
4.5537-45.7380.15571470.136826232770100
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)
11.1807-0.0956-0.41980.6905-0.23431.94850.0250.2809-0.0150.002-0.03620.15250.0559-0.41230.0130.172-0.07960.02110.3931-0.02260.249618.9114-56.93181.7886
21.68990.655-2.13780.2544-0.79044.15230.13850.49740.3396-0.01860.16380.2916-0.4293-1.0179-0.31250.2435-0.0140.04140.61020.04180.325712.7351-52.9519-1.582
38.91481.7439-6.02964.61410.41634.67640.03150.45320.2466-0.19380.28260.46750.2255-1.0371-0.32760.1479-0.04070.00150.5590.00520.37089.0622-56.4227-1.1171
41.093-0.0075-0.87060.81930.32211.84370.09780.2890.0377-0.0108-0.06540.1826-0.0067-0.487-0.00120.1809-0.07410.03110.4907-0.01310.300814.1971-57.73762.6456
50.00010.0235-0.00592.7263-0.71140.18590.1555-1.13170.65080.90930.03160.7978-0.3234-0.8624-0.12990.3835-0.00040.12810.640.09140.55178.2202-44.70788.7005
61.34530.54030.26710.6294-0.34190.5920.06330.1620.06950.148-0.04630.16850.0303-0.196-0.0240.1899-0.07690.03130.325-0.00620.248523.1519-56.64397.0005
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 25 )A1 - 25
2X-RAY DIFFRACTION2chain 'A' and (resid 26 through 34 )A26 - 34
3X-RAY DIFFRACTION3chain 'A' and (resid 35 through 42 )A35 - 42
4X-RAY DIFFRACTION4chain 'A' and (resid 43 through 69 )A43 - 69
5X-RAY DIFFRACTION5chain 'A' and (resid 70 through 74 )A70 - 74
6X-RAY DIFFRACTION6chain 'A' and (resid 75 through 114 )A75 - 114

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