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- PDB-2vud: PA-IIL lectin from pseudomonas aeruginosa complexed with fucose- ... -

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Basic information

Entry
Database: PDB / ID: 2vud
TitlePA-IIL lectin from pseudomonas aeruginosa complexed with fucose- derived glycomimetics
ComponentsFUCOSE-BINDING LECTIN PA-IIL
KeywordsSUGAR BINDING PROTEIN / LECTIN / PSEUDOMONAS AERUGINOSA / GLYCOMIMETICS / FUCOSE / SUGAR-BINDING PROTEIN
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
alpha-L-fucopyranose / Chem-LZ0 / Fucose-binding lectin PA-IIL
Similarity search - Component
Biological speciesPSEUDOMONAS AERUGINOSA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsBeha, S. / Marotte, K. / Sabin, C. / Mitchell, E.P. / Imberty, A. / Roy, R.
CitationJournal: To be Published
Title: Fucose-Derived Glycomimetics as High Affinity Ligands for Bacterial Lectin Pa-Iil from Pseudomonas Aeruginosa
Authors: Beha, S. / Marotte, K. / Sabin, C. / Mitchell, E.P. / Imberty, A. / Roy, R.
History
DepositionMay 22, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 21, 2009Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 8, 2017Group: Advisory / Source and taxonomy / Category: entity_src_gen / pdbx_unobs_or_zero_occ_atoms
Item: _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain
Revision 1.4Jul 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name / _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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Dec 13, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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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)48,47818
Polymers46,9394
Non-polymers1,53914
Water10,935607
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9330 Å2
ΔGint-78.2 kcal/mol
Surface area20430 Å2
MethodPQS
Unit cell
Length a, b, c (Å)53.079, 73.179, 55.367
Angle α, β, γ (deg.)90.00, 93.86, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
FUCOSE-BINDING LECTIN PA-IIL / PA-IIL LECTIN


Mass: 11734.707 Da / Num. of mol.: 4 / Fragment: RESIDUES 2-115
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PSEUDOMONAS AERUGINOSA (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9HYN5

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Sugars , 2 types, 4 molecules

#4: Sugar ChemComp-FUC / alpha-L-fucopyranose / alpha-L-fucose / 6-deoxy-alpha-L-galactopyranose / L-fucose / fucose


Type: L-saccharide, alpha linking / Mass: 164.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O5
IdentifierTypeProgram
LFucpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-L-fucopyranoseCOMMON NAMEGMML 1.0
a-L-FucpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
FucSNFG CARBOHYDRATE SYMBOLGMML 1.0
#5: Sugar ChemComp-LZ0 / [1-(2-oxoethyl)-1H-1,2,3-triazol-5-yl]methyl 6-deoxy-alpha-L-galactopyranoside / [1-(2-oxoethyl)-1H-1,2,3-triazol-5-yl]methyl 6-deoxy-alpha-L-galactoside / [1-(2-oxoethyl)-1H-1,2,3-triazol-5-yl]methyl 6-deoxy-L-galactoside / [1-(2-oxoethyl)-1H-1,2,3-triazol-5-yl]methyl 6-deoxy-galactoside


Type: L-saccharide / Mass: 287.269 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C11H17N3O6

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Non-polymers , 3 types, 617 molecules

#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 607 / 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: 1.88 Å3/Da / Density % sol: 46.17 % / Description: NONE
Crystal growpH: 8.5
Details: TRIS HCL 0.1M PH8.5, 1.75M AMMNONIUM SULFATE(THE PA-IIL/GLYCOMIMETIC COMPLEX WAS OBTAINED BY SOAKING METHOD FROM FUCOSE-CONTAINING CRYSTAL)

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Data collection

DiffractionMean temperature: 300 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC CCD / Detector: CCD / Date: Apr 26, 2006 / Details: TOROIDAL MIRROR
RadiationMonochromator: SINGLE CRYSTAL DIAMOND / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.7→44.11 Å / Num. obs: 46062 / % possible obs: 99.1 % / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Rmerge(I) obs: 0.16 / Net I/σ(I): 7.3
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 2.2 / % possible all: 98.5

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1UZV

1uzv


Resolution: 1.7→55.22 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.925 / SU B: 2.959 / SU ML: 0.097 / Cross valid method: THROUGHOUT / ESU R: 0.136 / ESU R Free: 0.116 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.218 2326 5.1 %RANDOM
Rwork0.203 ---
obs0.204 43714 99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.02 Å2
Baniso -1Baniso -2Baniso -3
1--0.18 Å20 Å20.27 Å2
2---0.46 Å20 Å2
3---0.68 Å2
Refinement stepCycle: LAST / Resolution: 1.7→55.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3308 0 89 607 4004
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0223538
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2451.9454844
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2925474
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.38326.883154
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.64315487
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6791510
X-RAY DIFFRACTIONr_chiral_restr0.0920.2609
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022703
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1860.21555
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2840.22486
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1350.2385
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1240.249
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1540.255
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.991.52367
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.323763
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.1431268
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.2774.51081
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.74 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.36 161
Rwork0.332 3180

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