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

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Basic information

Entry
Database: PDB / ID: 4ywa
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-4J9 / PA-I galactophilic lectin
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.192 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 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.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

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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)53,42710
Polymers51,0814
Non-polymers2,3466
Water13,403744
1
A: PA-I galactophilic lectin
B: PA-I galactophilic lectin
hetero molecules

C: PA-I galactophilic lectin
D: PA-I galactophilic lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,42710
Polymers51,0814
Non-polymers2,3466
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_656x+1,y,z+11
MethodPISA
2
C: PA-I galactophilic lectin
D: PA-I galactophilic lectin
hetero molecules

A: PA-I galactophilic lectin
B: PA-I galactophilic lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,42710
Polymers51,0814
Non-polymers2,3466
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_454x-1,y,z-11
MethodPISA
Unit cell
Length a, b, c (Å)40.770, 72.320, 78.710
Angle α, β, γ (deg.)117.230, 105.000, 89.940
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-4J9 / (2R,3R,4S,5R,6R,2'R,3'R,4'S,5'R,6'R)-2,2'-([(2R,3R,4S,5S,6S)-3,4-dihydroxy-6-(hydroxymethyl)tetrahydro-2H-pyran-2,5-diyl]bis{1H-1,2,3-triazole-1,4-diyl[(2S,3R,4S,5S,6S)-3,4-dihydroxy-6-(hydroxymethyl)tetrahydro-2H-pyran-2,5-diyl]-1H-1,2,3-triazole-1,4-diylmethanediyloxy})bis[6-(hydroxymethyl)tetrahydro-2H-pyran-3,4,5-triol]


Mass: 1092.970 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C40H60N12O24
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 744 / 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: 3.87 Å3/Da / Density % sol: 68.18 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.6 / Details: 1.5 M 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: 1.19→66.968 Å / Num. all: 229498 / Num. obs: 229498 / % possible obs: 94 % / Redundancy: 3.2 % / Biso Wilson estimate: 12.95 Å2 / Rpim(I) all: 0.042 / Rrim(I) all: 0.077 / Rsym value: 0.064 / Net I/av σ(I): 6.885 / Net I/σ(I): 6.8 / Num. measured all: 724110
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
1.19-1.262.80.9950.790126318360.7010.9951.189.3
1.26-1.333.10.6750.996920310960.4530.6751.791.9
1.33-1.423.40.4431.599092293750.2830.4432.692.8
1.42-1.543.10.2542.385865278070.1720.2543.893.8
1.54-1.693.10.1415.180177256680.0940.1415.694.7
1.69-1.883.40.0877.679855234910.0550.0878.895.7
1.88-2.1830.0679.163580209310.0460.06712.296.6
2.18-2.673.10.05710.955870177870.0380.05715.197.4
2.67-3.773.50.04314.848234138950.0270.04319.498.3
3.77-23.7363.20.03219.42439176120.0210.03220.398.7

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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: 1.192→23.736 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 24.87 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2035 11482 5.01 %
Rwork0.1858 217501 -
obs0.1867 228983 93.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 86.1 Å2 / Biso mean: 20.9891 Å2 / Biso min: 8.99 Å2
Refinement stepCycle: final / Resolution: 1.192→23.736 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3600 0 276 744 4620
Biso mean--45.1 33.59 -
Num. residues----484
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0113860
X-RAY DIFFRACTIONf_angle_d1.3895298
X-RAY DIFFRACTIONf_chiral_restr0.089594
X-RAY DIFFRACTIONf_plane_restr0.008680
X-RAY DIFFRACTIONf_dihedral_angle_d11.9991280
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.192-1.20550.36583660.36096685705186
1.2055-1.21970.34123830.34776701708487
1.2197-1.23460.37543630.3597028739190
1.2346-1.25020.32943580.31577010736891
1.2502-1.26670.36223540.3467019737391
1.2667-1.2840.30533500.30037103745391
1.284-1.30240.31643820.30976972735491
1.3024-1.32180.27893880.2847139752792
1.3218-1.34250.28073590.26087136749592
1.3425-1.36450.26224080.267178758693
1.3645-1.3880.27613790.26747106748592
1.388-1.41320.2553510.22647292764393
1.4132-1.44040.23714000.2257136753693
1.4404-1.46980.2424000.2217208760893
1.4698-1.50180.23093960.21127253764994
1.5018-1.53670.23533710.21847259763094
1.5367-1.57510.2193920.19687349774194
1.5751-1.61770.21883770.19187233761095
1.6177-1.66530.21653940.18357350774495
1.6653-1.7190.18853820.17267393777595
1.719-1.78040.21823840.17267367775195
1.7804-1.85170.17743740.16517425779996
1.8517-1.93590.18994050.18537400780596
1.9359-2.0380.183750.16457435781096
2.038-2.16560.17733850.16117469785497
2.1656-2.33260.17773930.16327475786897
2.3326-2.56710.18124040.16037546795097
2.5671-2.9380.18343780.17167612799098
2.938-3.69930.16253950.1557594798999
3.6993-23.74030.19234360.1627628806499

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