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

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Basic information

Entry
Database: PDB / ID: 2boj
Titlecrystal Structure of pseudomonas aeruginosa lectin (PA-IIL) complexed with methyl-B-D-Arabinopyranoside
ComponentsPSEUDOMONAS AERUGINOSA LECTIN II
KeywordsLECTIN / ARABINOSE / CALCIUM / LEWIS A / CYSTIC FIBROSIS
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
methyl beta-D-arabinopyranoside / Fucose-binding lectin PA-IIL
Similarity search - Component
Biological speciesPSEUDOMONAS AERUGINOSA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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.
History
DepositionApr 12, 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.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_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 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)48,01217
Polymers46,9394
Non-polymers1,07313
Water11,025612
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)50.636, 80.168, 52.517
Angle α, β, γ (deg.)90.00, 109.92, 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-ARW / methyl beta-D-arabinopyranoside / methyl beta-D-arabinoside / methyl D-arabinoside / methyl arabinoside


Type: D-saccharide / Mass: 164.156 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H12O5
IdentifierTypeProgram
DArap[1Me]bCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
1-methyl-b-D-arabinopyranoseCOMMON NAMEGMML 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.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 612 / 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: 1.74 Å3/Da / Density % sol: 29 %
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: ID14-2 / Wavelength: 0.933
DetectorType: ADSC CCD / Detector: CCD / Date: Jun 10, 2002 / 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: 1.8→29.6 Å / Num. obs: 35769 / % possible obs: 97.9 % / Redundancy: 3.73 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 7.5
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 3.45 % / Rmerge(I) obs: 0.19 / Mean I/σ(I) obs: 3.64 / % possible all: 89

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Processing

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

1uzv


Resolution: 1.8→49.39 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.945 / SU B: 2.129 / SU ML: 0.068 / Cross valid method: THROUGHOUT / ESU R: 0.118 / ESU R Free: 0.108 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. DISORDERED SIDE CHAINS ATOMS WERE MODELED WITH OCCUPANCIES LESS THAN 1.0
RfactorNum. reflection% reflectionSelection details
Rfree0.172 1116 3.1 %RANDOM
Rwork0.136 ---
obs0.137 34653 97.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 11.43 Å2
Baniso -1Baniso -2Baniso -3
1--0.05 Å20 Å20.01 Å2
2---0.03 Å20 Å2
3---0.1 Å2
Refinement stepCycle: LAST / Resolution: 1.8→49.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3308 0 57 612 3977
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0223538
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.321.9354881
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5215486
X-RAY DIFFRACTIONr_dihedral_angle_2_deg43.63727.179156
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.56815495
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.172158
X-RAY DIFFRACTIONr_chiral_restr0.0860.2614
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022740
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2220.21787
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3010.22553
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1540.2541
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1930.275
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1830.264
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6211.52387
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.05123832
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.75131248
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.8324.51049
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: 1.8→1.85 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.252 62
Rwork0.177 2134

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