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- PDB-4yw6: Structural Insight into Divalent Galactoside Binding to Pseudomon... -

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Basic information

Entry
Database: PDB / ID: 4yw6
TitleStructural Insight into Divalent Galactoside Binding to Pseudomonas aeruginosa lectin LecA
ComponentsPA-I galactophilic lectin
KeywordsSUGAR BINDING PROTEIN / Galactosides / lectins
Function / homology
Function and homology information


heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / carbohydrate binding / periplasmic space / cell surface / cytoplasm
Similarity search - Function
PA-IL-like / PA-IL-like protein / Galactose-binding lectin / Galactose-binding-like domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Chem-G0P / PA-I galactophilic lectin
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsVisini, R. / Jin, X. / Michaud, G. / Bergmann, M. / Gillon, E. / Imberty, A. / Stocker, A. / Darbre, T. / Pieters, R. / Reymond, J.-L.
CitationJournal: Acs Chem.Biol. / Year: 2015
Title: Structural Insight into Multivalent Galactoside Binding to Pseudomonas aeruginosa Lectin LecA.
Authors: Visini, R. / Jin, X. / Bergmann, M. / Michaud, G. / Pertici, F. / Fu, O. / Pukin, A. / Branson, T.R. / Thies-Weesie, D.M. / Kemmink, J. / Gillon, E. / Imberty, A. / Stocker, A. / Darbre, T. ...Authors: Visini, R. / Jin, X. / Bergmann, M. / Michaud, G. / Pertici, F. / Fu, O. / Pukin, A. / Branson, T.R. / Thies-Weesie, D.M. / Kemmink, J. / Gillon, E. / Imberty, A. / Stocker, A. / Darbre, T. / Pieters, R.J. / Reymond, J.L.
History
DepositionMar 20, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Sep 9, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 2, 2015Group: Database references
Revision 1.2Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PA-I galactophilic lectin
B: PA-I galactophilic lectin
C: PA-I galactophilic lectin
D: PA-I galactophilic lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,16712
Polymers51,0814
Non-polymers2,0868
Water16,177898
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6140 Å2
ΔGint-3 kcal/mol
Surface area20020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.870, 72.980, 79.020
Angle α, β, γ (deg.)117.520, 104.990, 90.000
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
PA-I galactophilic lectin / PA-IL / Galactose-binding lectin


Mass: 12770.137 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: lecA, pa1L, PA2570 / Production host: Escherichia coli (E. coli) / References: UniProt: Q05097
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-G0P / N-[(2S)-6-amino-1-oxo-1-(pyrrolidin-1-yl)hexan-2-yl]-4-(beta-D-galactopyranosyloxy)benzamide


Mass: 481.539 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C23H35N3O8
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 898 / 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: 3.91 Å3/Da / Density % sol: 68.58 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.6 / Details: 1.5M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.00003 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Oct 9, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00003 Å / Relative weight: 1
ReflectionResolution: 1.4→67.032 Å / Num. all: 129508 / Num. obs: 129508 / % possible obs: 84.9 % / Redundancy: 2.9 % / Biso Wilson estimate: 10.45 Å2 / Rpim(I) all: 0.04 / Rrim(I) all: 0.071 / Rsym value: 0.058 / Net I/av σ(I): 4.983 / Net I/σ(I): 7.7 / Num. measured all: 380562
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
1.4-1.482.90.2671.153158180560.1940.2673.581.1
1.48-1.572.80.221.143973156370.1680.22474.1
1.57-1.672.90.0877.153820188220.0610.0875.694.9
1.67-1.813.20.0825.156121176140.0540.0827.295.5
1.81-1.9830.1092.535286117220.0760.1098.268.9
1.98-2.212.60.0752.932745128160.060.0759.383.8
2.21-2.562.90.0634.333615117820.0450.06310.786.7
2.56-3.133.20.0510.233324105670.0330.0512.292.7
3.13-4.433.10.0413.22427977340.0260.0413.487.5
4.43-23.93430.03413.51424147580.0240.0341398.6

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Processing

Software
NameVersionClassification
SCALA3.3.21data scaling
PHENIXrefinement
PDB_EXTRACT3.15data extraction
MOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1oko

1oko


Resolution: 1.4→23.934 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 21.43 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2058 1961 1.54 %
Rwork0.1861 125153 -
obs0.1864 127114 83.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 81.37 Å2 / Biso mean: 18.9842 Å2 / Biso min: 4.8 Å2
Refinement stepCycle: final / Resolution: 1.4→23.934 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3604 0 280 898 4782
Biso mean--41.5 30.73 -
Num. residues----484
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093847
X-RAY DIFFRACTIONf_angle_d1.3795263
X-RAY DIFFRACTIONf_chiral_restr0.082569
X-RAY DIFFRACTIONf_plane_restr0.007690
X-RAY DIFFRACTIONf_dihedral_angle_d13.4621311
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.4-1.4350.2771510.21349774992591
1.435-1.47380.41511200.4117099721967
1.4738-1.51720.31381070.2837286739367
1.5172-1.56610.24251290.27917558768771
1.5661-1.62210.2141590.1623101091026895
1.6221-1.6870.17311530.1446103091046295
1.687-1.76380.19641610.1649101071026895
1.7638-1.85670.15831530.1542102651041896
1.8567-1.9730.2035920.22525551564352
1.973-2.12530.23421240.20378422854678
2.1253-2.3390.22411360.18648678881481
2.339-2.6770.19331490.1768101691031897
2.677-3.37130.20061620.1726101991036198
3.3713-23.93790.17431650.16149627979290

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