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- PDB-2bp6: crystal Structure of pseudomonas aeruginosa lectin (PA-IIL) compl... -

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Basic information

Entry
Database: PDB / ID: 2bp6
Titlecrystal Structure of pseudomonas aeruginosa lectin (PA-IIL) complexed with a-L-Galactopyranoside
ComponentsPSEUDOMONAS AERUGINOSA LECTIN II
KeywordsLECTIN / GALACTOSE / CALCIUM / PSEUDOMONAS AERUGINOSA
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-galactopyranose / Fucose-binding lectin PA-IIL
Similarity search - Component
Biological speciesPSEUDOMONAS AERUGINOSA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsSabin, C.D. / Mitchell, E.P. / Wimmerova, M. / Imberty, A.
Citation
Journal: FEBS Lett. / Year: 2006
Title: Binding of Different Monosaccharides by Lectin Pa-Iil from Pseudoman Aeruginosa: Thermodynamics Data Correlated with X-Ray Structures.
Authors: Sabin, C.D. / Mitchell, E.P. / Pokarna, M. / Gautier, C. / Utille, J.-P. / Wimmerova, M. / Imberty, A.
#1: Journal: Proteins: Struct.,Funct., Genet. / Year: 2005
Title: High Affinity Fucose Binding of Pseudomonas Aeruginosa Lectin Pa-Iil: 1.0 A Resolution Crystal Structure of the Complex Combined with Thermodynamics and Computational Chemistry Approaches
Authors: Mitchell, E. / Sabin, C.D. / Snajdrova, L. / Pokorna, M. / Perret, S. / Gautier, C. / Hofr, C. / Gilboa-Garber, N. / Koca, J. / Wimmerova, M. / Imberty, A.
#2: 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.M. / Gilboa-Garber, N. / Imberty, A.
History
DepositionApr 18, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 22, 2006Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 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.name / _chem_comp.type ..._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_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 / _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 1.4Dec 13, 2023Group: 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 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: 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)48,17218
Polymers46,9394
Non-polymers1,23314
Water7,746430
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)52.629, 72.790, 54.530
Angle α, β, γ (deg.)90.00, 94.38, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
PSEUDOMONAS AERUGINOSA LECTIN II / PA-IIL


Mass: 11734.707 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PSEUDOMONAS AERUGINOSA (bacteria) / Strain: PAO1 / Plasmid: PET25PAIIL / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9HYN5
#2: Sugar
ChemComp-GXL / alpha-L-galactopyranose / alpha-L-galactose / L-galactose / galactose


Type: L-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
LGalpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-L-galactopyranoseCOMMON NAMEGMML 1.0
a-L-GalpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GalSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical
ChemComp-CA / CALCIUM ION


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


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


Mass: 18.015 Da / Num. of mol.: 430 / 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: 1.9 Å3/Da / Density % sol: 34.72 %
Crystal growpH: 8.5
Details: TRIS HCL 0.1M, PH8.5, 1.75 M AMMONIUM SULFATE, pH 8.50

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.932
DetectorType: ADSC CCD / Detector: CCD / Date: Mar 17, 2003 / Details: MIRROR
RadiationMonochromator: SINGLE CRYSTAL DIAMOND / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.932 Å / Relative weight: 1
ReflectionResolution: 1.5→19.43 Å / Num. obs: 63528 / % possible obs: 97 % / Redundancy: 3.82 % / Biso Wilson estimate: 10.28 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 10.35
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.23 / Mean I/σ(I) obs: 3.08 / % possible all: 95.1

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1UZV

1uzv


Resolution: 1.5→19.43 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.961 / SU B: 0.992 / SU ML: 0.038 / Cross valid method: THROUGHOUT / ESU R: 0.064 / ESU R Free: 0.064 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.166 1934 3 %RANDOM
Rwork0.143 ---
obs0.143 61594 96.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 10.22 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å20 Å20 Å2
2--0 Å20 Å2
3---0.03 Å2
Refinement stepCycle: LAST / Resolution: 1.5→19.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3308 0 66 430 3804
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0223532
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3981.9384874
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6485483
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.41527.161155
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.6315490
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.319158
X-RAY DIFFRACTIONr_chiral_restr0.0970.2617
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022724
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2210.21719
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3030.22582
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1310.2341
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1940.260
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2420.232
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7761.52368
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.28323817
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.02231250
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.1414.51057
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: 1.5→1.54 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.25 154
Rwork0.186 4426

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