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- PDB-6q8d: Structure of Fucosylated D-antimicrobial peptide SB15 in complex ... -

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Basic information

Entry
Database: PDB / ID: 6q8d
TitleStructure of Fucosylated D-antimicrobial peptide SB15 in complex with the Fucose-binding lectin PA-IIL at 1.630 Angstrom resolution
Components
  • Fucose-binding lectin
  • SB15
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
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: 1.63 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 1.3Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Fucose-binding lectin
B: SB15
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,3255
Polymers13,0382
Non-polymers2863
Water1,22568
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area650 Å2
ΔGint-25 kcal/mol
Surface area6690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.445, 51.445, 98.006
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number93
Space group name H-MP4222
Components on special symmetry positions
IDModelComponents
11A-422-

HOH

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Components

#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-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A069Q9V4, UniProt: Q9HYN5*PLUS
#2: Polypeptide(D) SB15


Mass: 1303.682 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: Fucosylated D-antimicrobial peptide SB15. Peptide not entirely resolved. Full sequence:(DLE)(DLY)(DAL)(DLE)(DLY)(DLY)(DLE)(DAL)(DLY)(DLY)(DTY)
Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / 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.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H14O6
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 68 / Source method: isolated from a natural source / Formula: H2O
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: 2.57 Å3/Da / Density % sol: 52.21 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M HEPES sodium pH 7.5, 1.4 M Sodium citrate tribasic dihydrate

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.03679 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Aug 19, 2016
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03679 Å / Relative weight: 1
ReflectionResolution: 1.63→49.003 Å / Num. all: 17151 / Num. obs: 17151 / % possible obs: 99.8 % / Redundancy: 6.2 % / Rpim(I) all: 0.031 / Rrim(I) all: 0.077 / Rsym value: 0.071 / Net I/av σ(I): 8.2 / Net I/σ(I): 14 / Num. measured all: 106444
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
1.63-1.7261.7460.51464624400.7781.9181.746199
1.72-1.826.21.1430.71446323150.4951.2491.1431.5100
1.82-1.956.10.621.31320221640.2720.6780.622.899.8
1.95-2.16.40.3362.31309120470.1430.3660.3365.1100
2.1-2.36.60.1874.21251118960.0780.2030.1878.799.8
2.3-2.586.40.1246.31099517270.0530.1350.12412.199.9
2.58-2.9860.07710914415280.0340.0840.0771999.8
2.98-3.646.50.03616.7858313300.0150.0390.03638.4100
3.64-5.155.80.02419.2615610540.0110.0270.02456.2100
5.15-49.0035.60.01828.636536500.0080.020.01862.599.8

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation3.77 Å48.95 Å
Translation3.77 Å48.95 Å

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Processing

Software
NameVersionClassificationNB
PHENIXrefinement
XDSdata reduction
SCALA3.3.22data scaling
PHASER2.6.0phasing
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.63→49.003 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.19 / Phase error: 33.83 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2379 1570 5.02 %
Rwork0.2133 29685 -
obs0.2147 17092 99.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 108.07 Å2 / Biso mean: 41.686 Å2 / Biso min: 19.99 Å2
Refinement stepCycle: final / Resolution: 1.63→49.003 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms875 0 15 68 958
Biso mean--35.48 42.08 -
Num. residues----122
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006898
X-RAY DIFFRACTIONf_angle_d0.8551231
X-RAY DIFFRACTIONf_chiral_restr0.058159
X-RAY DIFFRACTIONf_plane_restr0.004161
X-RAY DIFFRACTIONf_dihedral_angle_d5.24502
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6296-1.68220.46041420.44692632277498
1.6822-1.74230.45061480.40827322880100
1.7423-1.8120.42021390.3552687282699
1.812-1.89450.38041440.324626942838100
1.8945-1.99440.31791440.27352696284099
1.9944-2.11940.28611420.241927012843100
2.1194-2.2830.25631420.217526872829100
2.283-2.51270.25771420.198827162858100
2.5127-2.87630.22281410.199127162857100
2.8763-3.62370.21861410.17727082849100
3.6237-49.02510.17641450.17127162861100
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)
11.9404-0.3246-0.25613.32970.66284.07490.1872-0.22260.02210.4294-0.21460.2738-0.5211-0.58060.06770.3706-0.11180.06290.3418-0.06360.284319.29718.496613.2576
21.8825-1.69443.12842.3935-1.11328.53670.0908-0.42580.34290.0723-0.37340.1688-0.601-1.40160.25710.6013-0.07550.06550.5044-0.14320.339515.17912.668318.5309
35.46054.76811.86977.02595.02155.31480.0895-0.19640.05610.72020.2548-0.67590.24670.8315-0.28970.5881-0.2995-0.13010.47280.01530.360535.17148.168121.5134
48.27140.6922.29783.5479-0.33675.18130.4602-0.38030.02960.5557-0.49060.4978-0.4722-1.03620.04250.4305-0.05610.13170.5682-0.12860.311714.84234.806117.2619
54.71843.32916.51794.18663.8169.3388-0.0231-0.76130.7172-0.0943-0.28120.0617-1.1698-0.62670.18630.4524-0.07940.08940.3508-0.12880.320218.859314.506512.419
65.1611-4.6026-5.41475.83196.19316.75820.1251-0.69170.68270.42040.2394-0.9016-1.2420.0253-0.30990.9535-0.1204-0.03790.4342-0.12890.364626.753922.019415.7625
70.8259-1.0433-0.49311.44650.23714.10210.2014-0.14350.12070.2835-0.36480.078-0.322-0.13740.14570.2988-0.0625-0.00660.2081-0.01060.21324.55395.12198.2982
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 47 )A43 - 47
4X-RAY DIFFRACTION4chain 'A' and (resid 48 through 61 )A48 - 61
5X-RAY DIFFRACTION5chain 'A' and (resid 62 through 69 )A62 - 69
6X-RAY DIFFRACTION6chain 'A' and (resid 70 through 74 )A70 - 74
7X-RAY DIFFRACTION7chain 'A' and (resid 75 through 114 )A75 - 114

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