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- PDB-2jdy: Mutant (G24N) of Pseudomonas aeruginosa lectin II (PA-IIL) comple... -

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Basic information

Entry
Database: PDB / ID: 2jdy
TitleMutant (G24N) of Pseudomonas aeruginosa lectin II (PA-IIL) complexed with methyl-b-D-mannoyranoside
ComponentsFUCOSE-BINDING LECTIN PA-IIL
KeywordsLECTIN / GLYCOMIMETIC / 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 alpha-D-mannopyranoside / Fucose-binding lectin PA-IIL
Similarity search - Component
Biological speciesPSEUDOMONAS AERUGINOSA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsAdam, J. / Pokorna, M. / Sabin, C. / Mitchell, E.P. / Imberty, A. / Wimmerova, M.
Citation
Journal: Bmc Struct.Biol. / Year: 2007
Title: Engineering of Pa-Iil Lectin from Pseudomonas Aeruginosa - Unravelling the Role of the Specificity Loop for Sugar Preference.
Authors: Adam, J. / Pokorna, M. / Sabin, C. / Mitchell, E.P. / Imberty, A. / Wimmerova, M.
#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.
#2: Journal: FEBS Lett. / Year: 2006
Title: Binding of Different Monosaccharides by Lectin Pa-Iil from Pseudomonas Aeruginosa: Thermodynamics Data Correlated with X-Ray Structures.
Authors: Sabin, C. / Mitchell, E. / Pokorna, M. / Gautier, C. / Utille, J. / Wimmerova M, M. / Imberty, A.
#3: Journal: Biochemistry / Year: 2006
Title: Unusual Entropy-Driven Affinity of Chromobacterium Violaceum Lectin Cv-Iil Toward Fucose and Mannose.
Authors: Pokorna, M. / Cioci, G. / Perret, S. / Rebuffet, E. / Kostlanova, N. / Adam, J. / Gilboa-Garber, N. / Mitchell, E. / Imberty, A. / Wimmerova, M.
#4: Journal: Mol.Microbiol. / Year: 2004
Title: A New Ralstonia Solanacearum High-Affinity Mannose- Binding Lectin Rs-Iil Structurally Resembling the Pseudomonas Aeruginosa Fucose-Specific Lectin Pa- Iil
Authors: Sudakevitz, D. / Kostlanova, N. / Blatmanjan, G. / Mitchell, E. / Lerrer, B. / Wimmerova, M. / Katcoff, D. / Imberty, A. / Gilboagarber, N.
History
DepositionJan 12, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 12, 2007Provider: 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_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: 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)48,78916
Polymers47,6924
Non-polymers1,09712
Water8,017445
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)50.383, 80.085, 52.493
Angle α, β, γ (deg.)90.00, 109.55, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 11922.956 Da / Num. of mol.: 4 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PSEUDOMONAS AERUGINOSA (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9HYN5
#2: Sugar
ChemComp-MMA / methyl alpha-D-mannopyranoside / O1-METHYL-MANNOSE / methyl alpha-D-mannoside / methyl D-mannoside / methyl mannoside


Type: D-saccharide / Mass: 194.182 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C7H14O6
IdentifierTypeProgram
DManp[1Me]aCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
1-methyl-a-D-mannopyranoseCOMMON NAMEGMML 1.0
o1-methyl-mannoseIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 445 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, GLY 25 TO ASN ENGINEERED RESIDUE IN CHAIN B, GLY 25 TO ASN ...ENGINEERED RESIDUE IN CHAIN A, GLY 25 TO ASN ENGINEERED RESIDUE IN CHAIN B, GLY 25 TO ASN ENGINEERED RESIDUE IN CHAIN C, GLY 25 TO ASN ENGINEERED RESIDUE IN CHAIN D, GLY 25 TO ASN

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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: 2.13 Å3/Da / Density % sol: 42.2 %
Crystal growpH: 7.5
Details: 0.1 M HEPES (PH 7.5), 10% ISO-PROPANOL, 20% PEG 4000.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.987
DetectorType: ADSC CCD / Detector: CCD / Date: Apr 8, 2006 / Details: TOROIDAL MIRROR
RadiationMonochromator: SINGLE CRYSTAL DIAMOND / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 1.7→49.45 Å / Num. obs: 42206 / % possible obs: 97.8 % / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 20.1
Reflection shellResolution: 1.7→1.74 Å / Redundancy: 3 % / Rmerge(I) obs: 0.2 / Mean I/σ(I) obs: 6.6 / % possible all: 88.7

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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→49.45 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.945 / SU B: 1.673 / SU ML: 0.056 / Cross valid method: THROUGHOUT / ESU R: 0.099 / ESU R Free: 0.094 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.173 2117 5 %RANDOM
Rwork0.142 ---
obs0.143 40067 97.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 9.68 Å2
Baniso -1Baniso -2Baniso -3
1-0.13 Å20 Å2-0.18 Å2
2--0.07 Å20 Å2
3----0.31 Å2
Refinement stepCycle: LAST / Resolution: 1.7→49.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3324 0 60 445 3829
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0223517
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2571.9354846
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2195476
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.1627.25160
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.93515492
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.272158
X-RAY DIFFRACTIONr_chiral_restr0.0960.2614
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022715
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2080.21641
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2940.22538
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1060.2373
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1680.279
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1850.247
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7821.52355
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.27923785
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.14531244
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.1994.51061
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
Rfree0.283 129
Rwork0.207 2504

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