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- PDB-6q86: Structure of Fucosylated D-antimicrobial peptide SB4 in complex w... -

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Basic information

Entry
Database: PDB / ID: 6q86
TitleStructure of Fucosylated D-antimicrobial peptide SB4 in complex with the Fucose-binding lectin PA-IIL at 2.008 Angstrom resolution
Components
  • Fucose-binding lectin
  • SB4
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: 2.008 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
C: SB4
B: Fucose-binding lectin
D: SB4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,16412
Polymers26,5594
Non-polymers6058
Water2,432135
1
A: Fucose-binding lectin
C: SB4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,5826
Polymers13,2802
Non-polymers3024
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Fucose-binding lectin
D: SB4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,5826
Polymers13,2802
Non-polymers3024
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.600, 55.600, 150.621
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-370-

HOH

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Components

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Protein / Polypeptide(D) / Sugars , 3 types, 6 molecules ABCD

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


Mass: 11734.707 Da / Num. of mol.: 2
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) SB4


Mass: 1545.013 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Fucosylated D-antimicrobial peptide SB4 / 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: isolated from a genetically manipulated source
Formula: C8H14O6

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Non-polymers , 3 types, 141 molecules

#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / 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.: 135 / 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: 2.53 Å3/Da / Density % sol: 51.39 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 2.5 M Ammonium nitrate, 0.1 M BIS-TRIS propane pH 7.0

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.00003 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Mar 16, 2016
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00003 Å / Relative weight: 1
Reflection twinOperator: -h,-k,l / Fraction: 0.26
ReflectionResolution: 2.008→48.151 Å / Num. all: 18746 / Num. obs: 18746 / % possible obs: 99.8 % / Redundancy: 4.8 % / Rpim(I) all: 0.014 / Rrim(I) all: 0.031 / Rsym value: 0.028 / Net I/av σ(I): 19.9 / Net I/σ(I): 30.1 / Num. measured all: 90867
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
2.01-2.124.80.352.21276126470.1760.3930.354.499.7
2.12-2.255.10.2263.51311625560.110.2520.2266.9100
2.25-2.45.10.1485.31221024140.0730.1650.14810.3100
2.4-2.5950.0968.11112122430.0480.1070.09614.8100
2.59-2.844.60.05713.5941720500.030.0650.05722.798.9
2.84-3.184.80.03421.7898218640.0170.0390.03437.999.9
3.18-3.6750.02230.8843416990.0110.0250.02261.699.9
3.67-4.494.70.01837.4680914350.0090.020.01875.299.8
4.49-6.354.20.01541.9484011430.0080.0170.01577.299.4
6.35-48.1514.60.01343.331776950.0070.0140.01384.199.6

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation3.58 Å48.15 Å
Translation3.58 Å48.15 Å

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
SCALA3.3.22data scaling
PHASER2.7.16phasing
PHENIXrefinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1OXC

1oxc


Resolution: 2.008→48.151 Å / Cross valid method: THROUGHOUT / σ(F): 7.54 / Phase error: 29.08 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.19 1737 5.03 %
Rwork0.1565 32784 -
obs0.163 18701 99.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 104.32 Å2 / Biso mean: 47.3571 Å2 / Biso min: 22.14 Å2
Refinement stepCycle: final / Resolution: 2.008→48.151 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1842 0 32 135 2009
Biso mean--44.66 50.3 -
Num. residues----254
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0141892
X-RAY DIFFRACTIONf_angle_d0.8352582
X-RAY DIFFRACTIONf_chiral_restr0.056330
X-RAY DIFFRACTIONf_plane_restr0.004334
X-RAY DIFFRACTIONf_dihedral_angle_d6.6291046
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.0084-2.06750.30261500.25762766291694
2.0675-2.13420.26591430.25172707285095
2.1342-2.21050.25881470.22782738288595
2.2105-2.2990.27691440.23922760290495
2.299-2.40360.27651410.22582750289195
2.4036-2.53030.21631460.21782796294295
2.5303-2.68880.22281410.20552705284695
2.6888-2.89640.23581390.19582609274890
2.8964-3.18780.1831480.17372745289395
3.1878-3.64890.16191450.14372750289595
3.6489-4.59660.17041440.12432756290095
4.5966-45.87630.17051390.11852702284194
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)
12.27220.5211-1.41983.40190.90942.98760.1572-0.1228-0.01320.37850.03060.28230.1261-0.4002-0.18770.3678-0.037-0.01030.35120.08350.2006-12.8978-10.09448.8624
25.246-2.2123-1.05974.59151.28461.9297-0.09110.00550.03421.06320.02250.42070.0874-0.73230.1720.5761-0.11380.03230.69560.2640.4898-18.9735-12.458413.2312
33.1089-0.2761.84752.4816-1.58473.3770.2873-0.2864-0.7532-0.04110.07390.39890.7951-0.5049-0.64830.5309-0.0947-0.04810.40470.09930.3442-11.8253-19.61325.8769
46.1992-2.92582.25272.88280.48263.70610.038-0.8525-0.74890.61950.79491.10450.3001-0.6855-0.75560.4628-0.04260.07820.51390.18520.4471-13.5397-8.886815.0467
52.24920.0529-1.38732.06980.07193.25990.2414-0.0043-0.07270.14610.27030.05250.1012-0.2589-0.32530.3164-0.0377-0.00910.27430.03050.1977-6.6494-4.7612.949
62.4441-0.5943-0.50141.6116-0.4632.19250.21340.0103-0.23620.2686-0.0550.21770.46010.1951-0.07480.4173-0.005-0.08050.31240.05570.2156-5.3944-12.33327.6156
71.14821.3021-0.25372.00430.60721.91770.3672-0.50490.14080.31740.186-0.6718-0.57030.9588-0.51120.6028-0.18350.12310.6144-0.26760.397812.58915.44828.2406
80.6288-0.6638-0.15321.4766-0.1310.45650.4188-0.2490.11690.39210.301-0.2715-0.6840.480.0550.8362-0.28340.29030.5414-0.42240.763310.723715.828110.3576
91.64360.82610.10073.23870.14242.33950.3478-0.51270.36760.24780.3399-0.6777-0.34840.7896-0.43080.5106-0.23660.10620.7168-0.34650.542614.37996.726410.4511
101.52290.12191.09742.21190.92991.14110.14050.03520.0550.09950.2904-0.3449-0.15540.4021-0.29710.3978-0.09940.06740.3628-0.08740.26614.98091.11692.5009
111.7605-0.2831.07430.4506-0.26270.68850.2451-0.29590.18060.00140.129-0.2891-0.79790.3584-0.36160.594-0.13690.15850.4142-0.14950.35434.31518.3347.7476
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 32 )A1 - 32
2X-RAY DIFFRACTION2chain 'A' and (resid 33 through 42 )A33 - 42
3X-RAY DIFFRACTION3chain 'A' and (resid 43 through 56 )A43 - 56
4X-RAY DIFFRACTION4chain 'A' and (resid 57 through 74 )A57 - 74
5X-RAY DIFFRACTION5chain 'A' and (resid 75 through 95 )A75 - 95
6X-RAY DIFFRACTION6chain 'A' and (resid 96 through 114 )A96 - 114
7X-RAY DIFFRACTION7chain 'B' and (resid 1 through 34 )B1 - 34
8X-RAY DIFFRACTION8chain 'B' and (resid 35 through 48 )B35 - 48
9X-RAY DIFFRACTION9chain 'B' and (resid 49 through 74 )B49 - 74
10X-RAY DIFFRACTION10chain 'B' and (resid 75 through 95 )B75 - 95
11X-RAY DIFFRACTION11chain 'B' and (resid 96 through 114 )B96 - 114

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