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- PDB-6q87: Structure of Fucosylated D-antimicrobial peptide SB10 in complex ... -

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Basic information

Entry
Database: PDB / ID: 6q87
TitleStructure of Fucosylated D-antimicrobial peptide SB10 in complex with the Fucose-binding lectin PA-IIL at 2.541 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: 2.541 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_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.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.ptnr2_symmetry / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Jan 24, 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: SB10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,5826
Polymers13,2802
Non-polymers3024
Water21612
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area760 Å2
ΔGint-24 kcal/mol
Surface area7000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)130.200, 130.200, 49.623
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number180
Space group name H-MP6222

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Components

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Protein / Polypeptide(D) / Sugars , 3 types, 3 molecules AB

#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 Lectin B from Pseudomonas aeruginosa
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(DE3) (bacteria) / Variant (production host): Gold pLysS AG / References: UniProt: A0A069Q9V4, UniProt: Q9HYN5*PLUS
#2: Polypeptide(D) SB10


Mass: 1545.013 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.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H14O6

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Non-polymers , 3 types, 15 molecules

#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-NH2 / AMINO GROUP


Mass: 16.023 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NH2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 12 / 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: 4.57 Å3/Da / Density % sol: 73.09 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 5% v/v Tacsimate pH 7.0, 0.1 M HEPES pH 7.0 ,10% w/v Polyethylene glycol monomethyl ether 5,000

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.000031 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Jul 6, 2018
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.000031 Å / Relative weight: 1
ReflectionResolution: 2.54→45.419 Å / Num. obs: 15464 / % possible obs: 99.37 % / Redundancy: 6.99 % / Rrim(I) all: 0.076 / Net I/σ(I): 12.74
Reflection shellResolution: 2.5414→2.7006 Å / % possible all: 98

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation5.26 Å45.42 Å
Translation5.26 Å45.42 Å

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Processing

Software
NameVersionClassificationNB
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASER2.7.16phasing
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1OXC

1oxc


Resolution: 2.541→45.419 Å / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 29.66 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2573 773 5.01 %
Rwork0.2124 14656 -
obs0.2147 15429 99.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 118.69 Å2 / Biso mean: 69.0029 Å2 / Biso min: 42.22 Å2
Refinement stepCycle: final / Resolution: 2.541→45.419 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms918 0 16 12 946
Biso mean--74.3 54.08 -
Num. residues----127
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007943
X-RAY DIFFRACTIONf_angle_d0.9231290
X-RAY DIFFRACTIONf_chiral_restr0.054165
X-RAY DIFFRACTIONf_plane_restr0.004168
X-RAY DIFFRACTIONf_dihedral_angle_d6.337520
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5414-2.70060.37781280.33532396252498
2.7006-2.90910.26481270.25772453258099
2.9091-3.20180.28761270.247924442571100
3.2018-3.66490.2811290.209924602589100
3.6649-4.61670.24141330.1942438257199
4.6167-45.42640.23321290.192524652594100
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)
13.6909-0.5281-0.59542.63070.92311.91780.11760.65640.08450.0793-0.0557-0.33320.15370.78330.02590.5649-0.2503-0.09780.9150.07490.4422-18.649156.391851.4019
21.71930.4642-3.37095.3684-1.06066.60940.11860.2440.0716-0.18340.5796-0.41880.73420.3523-0.84490.58320.0078-0.09951.28450.00990.5543-12.446552.40548.0543
32.58640.5677-2.45595.9643-0.46076.624-0.3376-0.6989-0.11190.01731.1395-0.46730.3290.7672-0.91690.44180.147-0.08881.1811-0.08950.5008-8.611856.273349.411
41.9683-0.56830.53122.1668-1.75543.4988-0.0810.738-0.15720.03640.0267-0.3419-0.15350.6123-0.01280.4952-0.140.01050.99890.00730.5083-13.920357.161752.2274
56.4173-3.17230.76784.08140.83462.71430.06570.83850.22980.37210.0696-0.2669-0.03710.5641-0.17770.39-0.1469-0.00890.8423-0.00930.3726-23.347854.738254.8992
61.59310.2505-1.18872.94981.54972.0664-0.18730.2361-0.11560.5630.0637-0.6125-0.34270.2632-0.02090.4136-0.1593-0.07660.66340.01920.4476-18.942955.439758.9728
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 95 )A70 - 95
6X-RAY DIFFRACTION6chain 'A' and (resid 96 through 114 )A96 - 114

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