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- PDB-3dcq: LECB (PA-LII) in complex with the synthetic ligand 2G0 -

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Basic information

Entry
Database: PDB / ID: 3dcq
TitleLECB (PA-LII) in complex with the synthetic ligand 2G0
ComponentsFucose-binding lectin PA-IIL
KeywordsSUGAR BINDING PROTEIN / LECTIN / CARBOHYDRATE
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-2G0 / Fucose-binding lectin PA-IIL
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsJohansson, E.M. / Crusz, S.A. / Kolomiets, E. / Buts, L. / Kadam, R.U. / Cacciarini, M. / Bartels, K.M. / Diggle, S.P. / Camara, M. / Williams, P. ...Johansson, E.M. / Crusz, S.A. / Kolomiets, E. / Buts, L. / Kadam, R.U. / Cacciarini, M. / Bartels, K.M. / Diggle, S.P. / Camara, M. / Williams, P. / Loris, R. / Nativi, C. / Rosenau, F. / Jaeger, K.E. / Darbre, T. / Reymond, J.L.
CitationJournal: Chem.Biol. / Year: 2008
Title: Inhibition and dispersion of Pseudomonas aeruginosa biofilms by glycopeptide dendrimers targeting the fucose-specific lectin LecB.
Authors: Johansson, E.M. / Crusz, S.A. / Kolomiets, E. / Buts, L. / Kadam, R.U. / Cacciarini, M. / Bartels, K.M. / Diggle, S.P. / Camara, M. / Williams, P. / Loris, R. / Nativi, C. / Rosenau, F. / ...Authors: Johansson, E.M. / Crusz, S.A. / Kolomiets, E. / Buts, L. / Kadam, R.U. / Cacciarini, M. / Bartels, K.M. / Diggle, S.P. / Camara, M. / Williams, P. / Loris, R. / Nativi, C. / Rosenau, F. / Jaeger, K.E. / Darbre, T. / Reymond, J.L.
History
DepositionJun 4, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 13, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _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.pdbx_dist_value / _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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fucose-binding lectin PA-IIL
B: Fucose-binding lectin PA-IIL
C: Fucose-binding lectin PA-IIL
D: Fucose-binding lectin PA-IIL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,43416
Polymers46,9394
Non-polymers2,49512
Water6,125340
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8330 Å2
ΔGint-98 kcal/mol
Surface area15610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.32, 75.52, 99.03
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Fucose-binding lectin PA-IIL


Mass: 11734.707 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: lecB, PA3361 / Plasmid: pET22a / Production host: Escherichia coli (E. coli) / References: UniProt: Q9HYN5
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-2G0 / (2S)-1-[(2S)-6-amino-2-({[(2S,3S,4R,5S,6S)-3,4,5-trihydroxy-6-methyltetrahydro-2H-pyran-2-yl]acetyl}amino)hexanoyl]-N-[(1S)-1-carbamoyl-3-methylbutyl]pyrrolidine-2-carboxamide


Mass: 543.653 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C25H45N5O8
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 340 / 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: 2.04 Å3/Da / Density % sol: 39.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 30% PEG 8000, 150mM ammonium sulphate, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.801 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Oct 26, 2007 / Details: mirrors
RadiationMonochromator: SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.801 Å / Relative weight: 1
ReflectionResolution: 1.8→20 Å / Num. obs: 36055 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.4 % / Biso Wilson estimate: 13.13 Å2 / Rmerge(I) obs: 0.122 / Net I/σ(I): 14.73
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.488 / Mean I/σ(I) obs: 4.53 / Num. unique all: 3516 / % possible all: 99.3

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Processing

Software
NameVersionClassification
MAR345data collection
PHASERphasing
CNS1.2refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1OVP

1ovp


Resolution: 1.8→20 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2108 1792 -random
Rwork0.1763 ---
all0.178 35997 --
obs0.178 35997 98.8 %-
Displacement parametersBiso mean: 17.29 Å2
Refinement stepCycle: LAST / Resolution: 1.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3301 0 102 340 3743
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.010104
X-RAY DIFFRACTIONc_angle_d1.73026

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