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- PDB-1gzt: Pseudomonas aeruginosa lectin II (PA-IIL) together with fucose -

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Basic information

Entry
Database: PDB / ID: 1gzt
TitlePseudomonas aeruginosa lectin II (PA-IIL) together with fucose
ComponentsFUCOSE-SPECIFIC LECTIN
KeywordsLECTIN / SUGAR-BINDING PROTEIN / FUCOSE
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
alpha-L-fucopyranose / Fucose-binding lectin PA-IIL
Similarity search - Component
Biological speciesPSEUDOMONAS AERUGINOSA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsMitchell, E. / Imberty, A. / Gilboa-Garber, N.
CitationJournal: 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
DepositionJun 6, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 19, 2002Provider: 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_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 1.4May 1, 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 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-SPECIFIC LECTIN
B: FUCOSE-SPECIFIC LECTIN
C: FUCOSE-SPECIFIC LECTIN
D: FUCOSE-SPECIFIC LECTIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,44116
Polymers47,4644
Non-polymers97712
Water12,683704
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)52.660, 72.920, 54.560
Angle α, β, γ (deg.)90.00, 94.23, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
FUCOSE-SPECIFIC LECTIN / HYPOTHETICAL PROTEIN PA3361


Mass: 11865.905 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Details: CO-CRYSTALS WITH FUCOSE / Source: (natural) PSEUDOMONAS AERUGINOSA (bacteria) / References: UniProt: Q9HYN5
#2: 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.: 4
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
#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.: 704 / 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: 32 %
Crystal growpH: 8.5
Details: TRIS HCL 0.1M, PH8.5, 1.75 M AMMNONIUM SULFATE, pH 8.50
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mg/mlprotein1drop
2250 ug/mlfucose1drop
32 mMsalts1drop
41.75 Mammonium sulfate1reservoir
50.1 MTris-HCl1reservoirpH8.5

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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: Jan 15, 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: 1.3→30 Å / Num. obs: 96602 / % possible obs: 95.7 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.049 / Net I/σ(I): 9.7
Reflection shellResolution: 1.3→1.35 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.301 / Mean I/σ(I) obs: 2.4 / % possible all: 70.9
Reflection
*PLUS
Lowest resolution: 30 Å / % possible obs: 95.8 % / Num. measured all: 324838
Reflection shell
*PLUS
% possible obs: 70.9 %

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Processing

Software
NameVersionClassification
REFMAC5refinement
HKLdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: HO DERIVATIVE SOLVED WITH (REMOTE ENERGY) SAD

Resolution: 1.3→30.02 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.969 / SU B: 1.018 / SU ML: 0.042 / Cross valid method: THROUGHOUT / ESU R: 0.044 / ESU R Free: 0.046 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.158 4818 5 %RANDOM
Rwork0.136 ---
obs0.137 91756 95.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 8.24 Å2
Baniso -1Baniso -2Baniso -3
1--0.46 Å20 Å2-0.1 Å2
2--0.15 Å20 Å2
3---0.3 Å2
Refinement stepCycle: LAST / Resolution: 1.3→30.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3308 0 52 704 4064
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0213642
X-RAY DIFFRACTIONr_bond_other_d0.0010.023156
X-RAY DIFFRACTIONr_angle_refined_deg1.5471.9265144
X-RAY DIFFRACTIONr_angle_other_deg1.08637343
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3923560
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.37115537
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.3040.2627
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024355
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02683
X-RAY DIFFRACTIONr_nbd_refined0.2440.3703
X-RAY DIFFRACTIONr_nbd_other0.2170.33043
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other1.1370.52
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2150.5556
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.2470.52
X-RAY DIFFRACTIONr_metal_ion_refined0.0650.523
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.4640.340
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2930.364
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.4380.591
X-RAY DIFFRACTIONr_symmetry_hbond_other0.2220.54
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6861.52410
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.27424047
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.04131232
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.1454.51097
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: 1.3→1.33 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.237 244
Rwork0.224 4807
Refinement
*PLUS
% reflection Rfree: 5 % / Rfactor Rfree: 0.158 / Rfactor Rwork: 0.136
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.006
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.26

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