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- PDB-6q77: Structure of Fucosylated D-antimicrobial peptide SB12 in complex ... -

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Basic information

Entry
Database: PDB / ID: 6q77
TitleStructure of Fucosylated D-antimicrobial peptide SB12 in complex with the Fucose-binding lectin PA-IIL at 2.002 Angstrom resolution
Components
  • Fucose-binding lectin
  • SB12
KeywordsANTIBIOTIC / Antimicrobial / Lectin / Complex
Function / homology
Function and homology information


single-species biofilm formation / carbohydrate binding / metal ion binding
Similarity search - Function
Lectin, sugar-binding / Calcium-mediated lectin / 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) / 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: 2.002 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 12, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Fucose-binding lectin
B: SB12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,9055
Polymers12,6192
Non-polymers2863
Water50428
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area310 Å2
ΔGint-12 kcal/mol
Surface area6820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.518, 51.518, 97.905
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number93
Space group name H-MP4222

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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) SB12


Mass: 884.163 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: Fucosylated D-antimicrobial peptide SB12 incompletely resolved. Full sequence:(DLE)(DLY)(DAL)(DLE)(DLY)(DLY)(DLE)(DAL)(DLY)(DLY)(DTY)(DLY)
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 / Water


Mass: 18.015 Da / Num. of mol.: 28 / 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: 2.57 Å3/Da / Density % sol: 52.21 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2 M Sodium acetate trihydrate, 0.1 M Sodium cacodylate trihydrate pH 6.5, 30% w/v Polyethylene glycol 8,000

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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: 2.002→48.952 Å / Num. all: 9462 / Num. obs: 9462 / % possible obs: 99.9 % / Redundancy: 6.3 % / Rpim(I) all: 0.021 / Rrim(I) all: 0.054 / Rsym value: 0.049 / Net I/av σ(I): 11.3 / Net I/σ(I): 19.1 / Num. measured all: 59614
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
2-2.116.60.8081873113230.3370.8780.8082.299.8
2.11-2.246.60.471.7849612810.1960.510.473.799.8
2.24-2.396.60.2742.8787511980.1140.2970.2745.799.9
2.39-2.586.30.2293.4715211330.0980.250.2296.8100
2.58-2.835.90.1475.3609110370.0660.1610.14710.299.9
2.83-3.166.50.0779.961809540.0320.0830.07718.8100
3.16-3.656.40.03718.554718510.0160.040.0373699.9
3.65-4.486.10.02326.444357250.010.0250.02351.699.9
4.48-6.335.40.01922.331865920.0090.0210.01961.599.5
6.33-48.9525.40.01831.519973680.0080.020.01868.699.2

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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
XDSdata reduction
SCALA3.3.22data scaling
PHASER2.6.0phasing
PHENIXrefinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.002→48.952 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.3 / Phase error: 36.56 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2672 823 4.87 %
Rwork0.2182 16074 -
obs0.2206 9403 99.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 124.28 Å2 / Biso mean: 62.0982 Å2 / Biso min: 31.98 Å2
Refinement stepCycle: final / Resolution: 2.002→48.952 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms872 0 15 28 915
Biso mean--55.16 52.94 -
Num. residues----122
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011895
X-RAY DIFFRACTIONf_angle_d0.9371226
X-RAY DIFFRACTIONf_chiral_restr0.063158
X-RAY DIFFRACTIONf_plane_restr0.004161
X-RAY DIFFRACTIONf_dihedral_angle_d6.127500
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 (%)
2.0015-2.12690.40791400.3872675281599
2.1269-2.29120.41181350.31762657279299
2.2912-2.52170.3071350.27962676281199
2.5217-2.88660.35091320.25626962828100
2.8866-3.63660.31321400.214126882828100
3.6366-48.96710.18751410.16642682282399
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)
15.3890.6180.14040.4791-0.99414.4656-0.131-1.1212-0.2970.09150.06820.0740.5124-0.13480.01490.52440.13760.06130.70490.09040.424267.956746.210915.2574
24.97321.4612-1.65111.5582-0.25786.368-0.2999-0.7003-0.40960.4240.10340.14780.643-0.75260.10540.44880.08920.05680.62480.08750.401767.726445.327512.3516
33.27271.9554-1.35351.3064-0.66954.2936-0.5032-0.9088-0.12570.45710.40890.364-0.2107-0.04450.07110.35260.0405-0.00060.5442-0.04010.350270.111453.52518.1312
41.57870.4054-1.50062.86231.77023.2396-0.3581-0.805-0.00520.34060.0746-0.51310.3523-0.00720.24630.45720.2011-0.02920.59530.07030.509476.852244.834512.3206
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 47 )A1 - 47
2X-RAY DIFFRACTION2chain 'A' and (resid 48 through 83 )A48 - 83
3X-RAY DIFFRACTION3chain 'A' and (resid 84 through 104 )A84 - 104
4X-RAY DIFFRACTION4chain 'A' and (resid 105 through 114 )A105 - 114

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