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- PDB-1w8h: structure of pseudomonas aeruginosa lectin II (PA-IIL)complexed w... -

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Basic information

Entry
Database: PDB / ID: 1w8h
Titlestructure of pseudomonas aeruginosa lectin II (PA-IIL)complexed with lewisA trisaccharide
ComponentsPSEUDOMONAS AERUGINOSA LECTIN II
KeywordsSUGAR BINDING PROTEIN / LECTIN / SUGAR / LEWIS A / CYSTIC FIBROSIS
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
Fucose-binding lectin PA-IIL
Similarity search - Component
Biological speciesPSEUDOMONAS AERUGINOSA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsPerret, S. / Sabin, C. / Dumon, C. / Budova, M. / Gautier, C. / Galanina, O. / Ilia, S. / Bovin, N. / Nicaise, M. / Desmadril, M. ...Perret, S. / Sabin, C. / Dumon, C. / Budova, M. / Gautier, C. / Galanina, O. / Ilia, S. / Bovin, N. / Nicaise, M. / Desmadril, M. / Gilboa-Garber, N. / Wimmerova, M. / Mitchell, E.P. / Imberty, A.
Citation
Journal: Biochem.J. / Year: 2005
Title: Structural Basis for the Interaction between Human Milk Oligosaccharides and the Bacterial Lectin Pa-Iil of Pseudomonas Aeruginosa.
Authors: Perret, S. / Sabin, C. / Dumon, C. / Pokorna, M. / Gautier, C. / Galanina, O. / Ilia, S. / Bovin, N. / Nicaise, M. / Desmadril, M. / Gilboa-Garber, N. / Wimmerova, M. / Mitchell, E.P. / Imberty, A.
#1: Journal: Nat.Struct.Biol. / Year: 2002
Title: Structural Basis for Oligosaccharide-Mediated Adhesion of Pseudomonas Aeruginosa in the Lungs of Cystic Fibrosis Patients.
Authors: Mitchell, E. / Houles, C. / Sudakevitz, D. / Wimmerova, M. / Gautier, C. / Perez, S. / Wu, A. / Gilboa-Garber, N. / Imberty, A.
History
DepositionSep 21, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 31, 2005Provider: repository / Type: Initial release
Revision 1.1Jan 30, 2013Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Other / Source and taxonomy / Structure summary / Version format compliance
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / struct_asym / struct_conn / struct_conn_type / struct_sheet / struct_sheet_order / struct_sheet_range / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_alt_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_database_status.status_code_sf / _pdbx_struct_assembly_gen.asym_id_list / _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_asym_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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Feb 14, 2024Group: Data collection / Database references ...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
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 700 SHEET DETERMINATION METHOD: AUTHOR PROVIDED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PSEUDOMONAS AERUGINOSA LECTIN II
B: PSEUDOMONAS AERUGINOSA LECTIN II
C: PSEUDOMONAS AERUGINOSA LECTIN II
D: PSEUDOMONAS AERUGINOSA LECTIN II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,57421
Polymers47,4644
Non-polymers3,11017
Water7,891438
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11070 Å2
ΔGint-78.9 kcal/mol
Surface area20320 Å2
MethodPQS
Unit cell
Length a, b, c (Å)51.575, 75.824, 52.746
Angle α, β, γ (deg.)90.00, 93.48, 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
PSEUDOMONAS AERUGINOSA LECTIN II / PA-IIL


Mass: 11865.905 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: EACH MONOMER CONTAINS TWO CLOSE CALCIUM CATIONS THAT MEDIATE THE BINDING OF THE SACCHARIDE
Source: (gene. exp.) PSEUDOMONAS AERUGINOSA (bacteria) / Plasmid: PET25PA2L / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9HYN5

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Sugars , 3 types, 4 molecules

#2: Polysaccharide alpha-L-fucopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-3)-beta-D-galactopyranose- ...alpha-L-fucopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-3)-beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 732.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpa1-4DGlcpNAca1-3DGalpb1-3DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
[][b-D-GlcpNAc]{[(3+1)][b-D-Galp]{}[(4+1)][a-L-Fucp]{}}LINUCSPDB-CARE
#3: Polysaccharide beta-D-galactopyranose-(1-3)-[alpha-L-fucopyranose-(1-4)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 529.490 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGalpb1-3[LFucpa1-4]DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,3,2/[a2122h-1b_1-5_2*NCC/3=O][a2112h-1b_1-5][a1221m-1a_1-5]/1-2-3/a3-b1_a4-c1WURCSPDB2Glycan 1.1.0
[][b-D-GlcpNAc]{[(3+1)][b-D-Galp]{}[(4+1)][a-L-Fucp]{}}LINUCSPDB-CARE
#4: Polysaccharide beta-D-galactopyranose-(1-3)-[alpha-L-fucopyranose-(1-4)]2-acetamido-2-deoxy-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 529.490 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGalpb1-3[LFucpa1-4]DGlcpNAca1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,3,2/[a2122h-1a_1-5_2*NCC/3=O][a2112h-1b_1-5][a1221m-1a_1-5]/1-2-3/a3-b1_a4-c1WURCSPDB2Glycan 1.1.0
[][a-D-GlcpNAc]{[(3+1)][b-D-Galp]{}[(4+1)][a-L-Fucp]{}}LINUCSPDB-CARE

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Non-polymers , 4 types, 451 molecules

#5: Chemical
ChemComp-CA / CALCIUM ION


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


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 438 / 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: 2.2 Å3/Da / Density % sol: 44.3 %
Crystal growpH: 8.5 / Details: pH 8.50

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934
DetectorType: ADSC CCD / Detector: CCD / Date: Oct 28, 2003 / Details: MULTILAYER MIRROR
RadiationMonochromator: SINGLE CRYSTAL DIAMOND / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 1.75→26.82 Å / Num. obs: 34811 / % possible obs: 85.1 % / Observed criterion σ(I): 0 / Redundancy: 4.06 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 13.19
Reflection shellResolution: 1.75→1.81 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 3.76 / % possible all: 41.7

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Processing

Software
NameVersionClassification
REFMAC5.1.9999refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1GZT

1gzt


Resolution: 1.75→26.35 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.945 / SU B: 1.959 / SU ML: 0.064 / Cross valid method: THROUGHOUT / ESU R: 0.111 / ESU R Free: 0.108 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.169 730 2.1 %RANDOM
Rwork0.125 ---
obs0.126 34037 85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 9.68 Å2
Baniso -1Baniso -2Baniso -3
1-0.51 Å20 Å2-0.19 Å2
2---0.33 Å20 Å2
3----0.21 Å2
Refinement stepCycle: LAST / Resolution: 1.75→26.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3306 0 240 438 3984
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0223653
X-RAY DIFFRACTIONr_bond_other_d0.0010.023148
X-RAY DIFFRACTIONr_angle_refined_deg1.4581.9845022
X-RAY DIFFRACTIONr_angle_other_deg0.82937306
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8715464
X-RAY DIFFRACTIONr_dihedral_angle_2_deg44.78627.219151
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.29315482
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.783158
X-RAY DIFFRACTIONr_chiral_restr0.0940.2666
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024035
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02620
X-RAY DIFFRACTIONr_nbd_refined0.2220.2644
X-RAY DIFFRACTIONr_nbd_other0.1880.22995
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0820.22117
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1940.2301
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1550.215
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1780.256
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1890.236
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8791.52340
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.36223724
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.24231423
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.3114.51298
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: 1.75→1.79 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.2 26
Rwork0.165 1173

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