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- PDB-6s5s: Cfucosylated second generation peptide dendrimer SBD8 bound to Fu... -

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Basic information

Entry
Database: PDB / ID: 6s5s
TitleCfucosylated second generation peptide dendrimer SBD8 bound to Fucose binding Lectin LecB (PA-IIL) from Pseudomonas aeruginosa at 1.43 Angstrom resolution
Components
  • Fucose-binding lectin
  • SBD8 chain B
  • SBD8 chain C
  • SBD8 chain D
KeywordsSUGAR BINDING PROTEIN / Lectin / Fucosylated / Dendrimer / Second Generation
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
AMINO GROUP / Chem-ZDC / Fucose-binding lectin / Fucose-binding lectin PA-IIL
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
unidentified (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.433 Å
AuthorsBaeriswyl, S. / Stocker, A. / Reymond, J.-L.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science Foundation Switzerland
CitationJournal: Helv.Chim.Acta / Year: 2019
Title: X-Ray Crystal Structure of a Second Generation Peptide Dendrimer in Complex with Pseudomonas aeruginosa Lectin LecB
Authors: Baeriswyl, S. / Javor, S. / Stocker, A. / Darbre, T. / Reymond, J.-L.
History
DepositionJul 2, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 21, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Data collection / Derived calculations / Refinement description
Category: chem_comp / pdbx_struct_conn_angle ...chem_comp / pdbx_struct_conn_angle / refine / 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 / _refine.pdbx_diffrn_id / _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 1.2Jan 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: SBD8 chain B
C: SBD8 chain C
D: SBD8 chain D
E: SBD8 chain C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,4099
Polymers14,1075
Non-polymers3024
Water2,864159
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1660 Å2
ΔGint-25 kcal/mol
Surface area7590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.297, 106.297, 57.090
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number177
Space group name H-MP622
Components on special symmetry positions
IDModelComponents
11A-520-

HOH

21A-533-

HOH

31A-546-

HOH

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Components

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Protein/peptide , 3 types, 4 molecules BCED

#2: Protein/peptide SBD8 chain B


Mass: 806.007 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Cfucosylated peptide dendrimer SBD8, chain B / Source: (synth.) unidentified (others)
#3: Protein/peptide SBD8 chain C


Mass: 357.468 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Cfucosylated peptide dendrimer SBD8, chain C / Source: (synth.) unidentified (others)
#4: Protein/peptide SBD8 chain D


Mass: 719.914 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Cfucosylated peptide dendrimer SBD8, chain D / Source: (synth.) unidentified (others)

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Protein / Sugars , 2 types, 2 molecules A

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


Mass: 11865.905 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Fucose binding lectin LecB (PA-IIL) from Pseudomonas aeruginosa
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria)
Gene: lecB, C0044_25260, CAZ10_21840, DT376_00595, DY979_15445, ECC04_10105, EFK27_13700, EGV95_09240, EGY23_15550, IPC669_23070, PA5486_01888, 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
#7: 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 / Feature type: SUBJECT OF INVESTIGATION

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Non-polymers , 3 types, 162 molecules

#5: Chemical ChemComp-CA / CALCIUM ION


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


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


Mass: 18.015 Da / Num. of mol.: 159 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 3.32 Å3/Da / Density % sol: 62.99 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.1 M BIS-TRIS pH 6.5, 3.0 M Sodium chloride

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.000033 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: 1.000033 Å / Relative weight: 1
ReflectionResolution: 1.433→48.517 Å / Num. obs: 66042 / % possible obs: 99.5 % / Redundancy: 17.1 % / Biso Wilson estimate: 20.3 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.17 / Net I/σ(I): 14.8
Reflection shellResolution: 1.433→1.44 Å / Redundancy: 5.5 % / Mean I/σ(I) obs: 0.73 / Num. unique obs: 10408 / CC1/2: 0.247 / Rrim(I) all: 0.207 / % possible all: 99.7

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation4.94 Å48.52 Å
Translation4.94 Å48.52 Å

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
XSCALEdata scaling
PHASER2.8.1phasing
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1OXC

1oxc


Resolution: 1.433→48.517 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 17.96
RfactorNum. reflection% reflection
Rfree0.1785 3292 4.99 %
Rwork0.1628 --
obs0.1636 66035 99.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 89.33 Å2 / Biso mean: 20.9158 Å2 / Biso min: 5.5 Å2
Refinement stepCycle: final / Resolution: 1.433→48.517 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms977 0 5 159 1141
Biso mean--19.98 31.47 -
Num. residues----133
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.017994
X-RAY DIFFRACTIONf_angle_d1.5641349
X-RAY DIFFRACTIONf_chiral_restr0.162170
X-RAY DIFFRACTIONf_plane_restr0.012178
X-RAY DIFFRACTIONf_dihedral_angle_d17.03333
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 (%)
1.4329-1.45340.43851300.37292411254192
1.4534-1.47510.34561310.3472512264397
1.4751-1.49810.30081420.301426462788100
1.4981-1.52270.26631370.273725942731100
1.5227-1.54890.27191390.244826702809100
1.5489-1.57710.26051380.237326202758100
1.5771-1.60740.24061360.226426062742100
1.6074-1.64020.23221390.216926362775100
1.6402-1.67590.2271350.192826512786100
1.6759-1.71490.19471390.180526092748100
1.7149-1.75780.1761390.173525862725100
1.7578-1.80530.1831380.155826552793100
1.8053-1.85840.16171410.145926252766100
1.8584-1.91840.13951340.142226252759100
1.9184-1.9870.16541360.138426262762100
1.987-2.06650.18791350.130226272762100
2.0665-2.16060.15141390.126626302769100
2.1606-2.27450.16111350.129726312766100
2.2745-2.4170.12091420.128926232765100
2.417-2.60360.15631390.140326342773100
2.6036-2.86560.16081360.144726242760100
2.8656-3.28020.15011400.146626132753100
3.2802-4.13240.15371370.134226462783100
4.1324-48.54510.18221350.180426432778100
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)
12.263-0.2876-0.86750.4837-0.11541.4446-0.00050.01030.0504-0.00870.0026-0.079-0.00030.0077-0.00070.1184-0.0098-0.02290.0806-0.02020.0997-46.547212.12366.9707
27.3825-0.6153-0.46350.14550.4011.0858-0.0683-0.1355-0.00660.030.0937-0.0313-0.0320.0174-0.03230.1487-0.0013-0.00990.0709-0.00310.1265-47.703819.1619.5727
36.0665-2.3183-5.27311.7891.78454.6748-0.2803-0.3602-0.370.16530.1305-0.02240.18610.25590.06880.1450.0129-0.02160.17780.00240.1395-41.745911.560611.8519
46.35962.43331.45971.97641.05350.5722-0.3547-1.15770.69871.4075-0.04990.331-0.6297-0.66410.28040.4180.0879-0.03370.268-0.05840.1623-53.8815.450123.2521
50.8943-0.8096-0.54731.63051.37461.4837-0.0611-0.0419-0.00720.09050.06730.00390.0756-0.00310.00330.13190.0032-0.00420.08930.01090.0927-53.60916.88836.8228
62.463-0.0133-1.85080.790.24281.9639-0.07590.1220.0196-0.01780.0767-0.02250.0323-0.05250.00060.1464-0.0033-0.00240.1222-0.00220.1155-46.41812.2790.3297
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 56 )A26 - 56
3X-RAY DIFFRACTION3chain 'A' and (resid 57 through 69 )A57 - 69
4X-RAY DIFFRACTION4chain 'A' and (resid 70 through 74 )A70 - 74
5X-RAY DIFFRACTION5chain 'A' and (resid 75 through 104 )A75 - 104
6X-RAY DIFFRACTION6chain 'A' and (resid 105 through 114 )A105 - 114

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