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- PDB-6q85: Structure of Fucosylated D-antimicrobial peptide SB11 in complex ... -

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Basic information

Entry
Database: PDB / ID: 6q85
TitleStructure of Fucosylated D-antimicrobial peptide SB11 in complex with the Fucose-binding lectin PA-IIL at 1.990 Angstrom resolution
Components
  • Fucose-binding lectin
  • SB11
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: 1.99 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_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
E: SB11
B: Fucose-binding lectin
F: SB11
C: Fucose-binding lectin
G: SB11
D: Fucose-binding lectin
H: SB11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,81624
Polymers52,6068
Non-polymers1,20916
Water5,260292
1
A: Fucose-binding lectin
E: SB11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,4947
Polymers13,1522
Non-polymers3425
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area720 Å2
ΔGint-24 kcal/mol
Surface area6910 Å2
MethodPISA
2
B: Fucose-binding lectin
F: SB11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,4145
Polymers13,1522
Non-polymers2623
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area730 Å2
ΔGint-24 kcal/mol
Surface area6890 Å2
MethodPISA
3
C: Fucose-binding lectin
G: SB11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,4947
Polymers13,1522
Non-polymers3425
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area720 Å2
ΔGint-24 kcal/mol
Surface area6830 Å2
MethodPISA
4
D: Fucose-binding lectin
H: SB11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,4145
Polymers13,1522
Non-polymers2623
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area730 Å2
ΔGint-25 kcal/mol
Surface area6860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)132.785, 132.785, 190.554
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-423-

HOH

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Components

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Protein / Polypeptide(D) / Sugars , 3 types, 12 molecules ABCDEFGH

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


Mass: 11734.707 Da / Num. of mol.: 4
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)
SB11


Mass: 1416.840 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: Fucosylated D-antimicrobial peptide SB11 / 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.: 4
Source method: isolated from a genetically manipulated source
Formula: C8H14O6

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Non-polymers , 3 types, 304 molecules

#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca
#5: Chemical
ChemComp-NH2 / AMINO GROUP


Mass: 16.023 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: NH2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 292 / 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

Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 0.2 M Ammonium acetate, 0.1 M Sodium citrate tribasic dihydrate pH 5.6, 30% v/v (+/-)-2-Methyl-2,4-pentanediol

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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 20, 2016
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03679 Å / Relative weight: 1
ReflectionResolution: 1.99→45.897 Å / Num. all: 68307 / Num. obs: 68307 / % possible obs: 99.8 % / Redundancy: 9.8 % / Rpim(I) all: 0.048 / Rrim(I) all: 0.15 / Rsym value: 0.142 / Net I/av σ(I): 4.7 / Net I/σ(I): 10 / Num. measured all: 667381
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
1.99-2.19.82.0150.49479096960.6752.1272.0151.298.8
2.1-2.2210.21.3370.69506393000.4391.4081.3371.8100
2.22-2.3810.10.8480.98866587700.280.8930.8482.899.9
2.38-2.579.80.5591.48045581870.1870.590.5594100
2.57-2.819.10.3312.36894175770.1160.3510.3316.1100
2.81-3.15100.184.26852168700.060.190.1810.7100
3.15-3.6310.10.0997.26178261170.0330.1050.09919.4100
3.63-4.459.60.0669.75018652280.0230.070.06627.5100
4.45-6.298.60.0511.23561541270.0180.0530.0531.2100
6.29-45.8979.60.03414.52336324350.0120.0360.03436.299.8

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation6.47 Å45.9 Å
Translation6.47 Å45.9 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
Starting model: 1OXC

1oxc


Resolution: 1.99→45.897 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 23.96 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2193 3404 5 %
Rwork0.173 64731 -
obs0.1753 68135 99.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 126.58 Å2 / Biso mean: 45.0036 Å2 / Biso min: 24.73 Å2
Refinement stepCycle: final / Resolution: 1.99→45.897 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3637 0 64 292 3993
Biso mean--44.69 50.57 -
Num. residues----504
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063737
X-RAY DIFFRACTIONf_angle_d0.7555117
X-RAY DIFFRACTIONf_chiral_restr0.058656
X-RAY DIFFRACTIONf_plane_restr0.003668
X-RAY DIFFRACTIONf_dihedral_angle_d5.0192061
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 24

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9896-2.0180.33811530.31352534268796
2.018-2.04820.37421530.282926222775100
2.0482-2.08020.33741330.270826672800100
2.0802-2.11430.29621240.25542640276499
2.1143-2.15070.29721330.23626792812100
2.1507-2.18980.27511340.218726432777100
2.1898-2.2320.22981300.198826812811100
2.232-2.27750.27311470.206326472794100
2.2775-2.3270.29441340.205526872821100
2.327-2.38120.28661450.202626472792100
2.3812-2.44070.28781390.201126942833100
2.4407-2.50670.27571420.195526702812100
2.5067-2.58050.23811490.189626752824100
2.5805-2.66370.26711420.181826812823100
2.6637-2.75890.22131420.174426862828100
2.7589-2.86940.24211460.173426872833100
2.8694-2.99990.21021240.161527192843100
2.9999-3.15810.23561390.155727212860100
3.1581-3.35590.19561670.151526902857100
3.3559-3.61490.15361360.13927352871100
3.6149-3.97850.21591480.144127492897100
3.9785-4.55370.17531690.142527502919100
4.5537-5.73550.16191420.155228212963100
5.7355-45.90880.22751330.186630063139100

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