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Entry
Database: PDB / ID: 4yw7
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-4J0 / beta-D-galactopyranose / PA-I galactophilic lectin
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.82 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 2.0Dec 11, 2019Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations
Category: atom_site / pdbx_distant_solvent_atoms ...atom_site / pdbx_distant_solvent_atoms / pdbx_nonpoly_scheme / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_oper_list / pdbx_validate_close_contact / pdbx_validate_symm_contact / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _pdbx_distant_solvent_atoms.auth_seq_id / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details / _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _pdbx_validate_symm_contact.auth_seq_id_1 / _pdbx_validate_symm_contact.auth_seq_id_2 / _struct_site.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id / _struct_site.pdbx_num_residues / _struct_site_gen.auth_asym_id / _struct_site_gen.auth_comp_id / _struct_site_gen.auth_seq_id / _struct_site_gen.label_asym_id / _struct_site_gen.label_comp_id / _struct_site_gen.label_seq_id / _struct_site_gen.pdbx_num_res / _struct_site_gen.site_id / _struct_site_gen.symmetry
Revision 2.1Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / 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_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.ptnr2_symmetry / _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_symmetry
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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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
E: PA-I galactophilic lectin
F: PA-I galactophilic lectin
G: PA-I galactophilic lectin
H: PA-I galactophilic lectin
I: PA-I galactophilic lectin
J: PA-I galactophilic lectin
K: PA-I galactophilic lectin
L: PA-I galactophilic lectin
M: PA-I galactophilic lectin
N: PA-I galactophilic lectin
O: PA-I galactophilic lectin
P: PA-I galactophilic lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)209,42346
Polymers204,32216
Non-polymers5,10130
Water33,7421873
1
A: PA-I galactophilic lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,9903
Polymers12,7701
Non-polymers2202
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: PA-I galactophilic lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,9903
Polymers12,7701
Non-polymers2202
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: PA-I galactophilic lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,9593
Polymers12,7701
Non-polymers1,1892
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: PA-I galactophilic lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,9903
Polymers12,7701
Non-polymers2202
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: PA-I galactophilic lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,9903
Polymers12,7701
Non-polymers2202
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: PA-I galactophilic lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,9903
Polymers12,7701
Non-polymers2202
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: PA-I galactophilic lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,9903
Polymers12,7701
Non-polymers2202
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
H: PA-I galactophilic lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,9903
Polymers12,7701
Non-polymers2202
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
9
I: PA-I galactophilic lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,9593
Polymers12,7701
Non-polymers1,1892
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
10
J: PA-I galactophilic lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,9903
Polymers12,7701
Non-polymers2202
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
11
K: PA-I galactophilic lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,9903
Polymers12,7701
Non-polymers2202
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
12
L: PA-I galactophilic lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,9903
Polymers12,7701
Non-polymers2202
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
13
M: PA-I galactophilic lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,8102
Polymers12,7701
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
14
N: PA-I galactophilic lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,9903
Polymers12,7701
Non-polymers2202
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
15
O: PA-I galactophilic lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,9903
Polymers12,7701
Non-polymers2202
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
16
P: PA-I galactophilic lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,8102
Polymers12,7701
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.570, 89.310, 100.010
Angle α, β, γ (deg.)90.040, 89.830, 79.610
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.: 16
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.: 16 / Source method: obtained synthetically / Formula: Ca
#3: Sugar
ChemComp-GAL / beta-D-galactopyranose / Galactose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGalpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-galactopyranoseCOMMON NAMEGMML 1.0
b-D-GalpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GalSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Chemical ChemComp-4J0 / (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-diylpropane-3,1-diyloxy})bis[6-(hydroxymethyl)tetrahydro-2H-pyran-3,4,5-triol]


Mass: 1149.077 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C44H68N12O24
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1873 / 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: 2.13 Å3/Da / Density % sol: 42.29 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 3.5 / Details: 0.1 M Citric acid, 3.0 M sodium chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.91956 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Apr 14, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91956 Å / Relative weight: 1
ReflectionResolution: 1.82→100.009 Å / Num. all: 134652 / Num. obs: 134652 / % possible obs: 89 % / Redundancy: 2.4 % / Biso Wilson estimate: 14.45 Å2 / Rpim(I) all: 0.067 / Rrim(I) all: 0.112 / Rsym value: 0.089 / Net I/av σ(I): 5.875 / Net I/σ(I): 6 / Num. measured all: 322703
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
1.82-1.922.50.3372.249457195890.2410.3372.488.4
1.92-2.032.50.2243.346456184160.1620.2243.588
2.03-2.182.50.1734.242856173150.1260.1734.488
2.18-2.352.50.1444.939982159810.1030.1445.187.4
2.35-2.572.40.1195.635526147820.0880.1195.888.1
2.57-2.8820.0986.427535134820.0780.0986.588.4
2.88-3.321.90.0717.522136119630.0620.071889.2
3.32-4.072.40.0559.725925106150.0420.05511.393.8
4.07-5.762.60.0519.82165982280.0380.05112.494.2
5.76-16.0342.60.05310.21117142810.0380.05311.489.2

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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: OKO1

Resolution: 1.82→16.034 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 23.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2206 6652 4.94 %
Rwork0.1789 127942 -
obs0.1809 134594 89.07 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 74.08 Å2 / Biso mean: 18.9013 Å2 / Biso min: 1.95 Å2
Refinement stepCycle: final / Resolution: 1.82→16.034 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14332 0 456 1873 16661
Biso mean--29.27 25.38 -
Num. residues----1936
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00615020
X-RAY DIFFRACTIONf_angle_d0.84220575
X-RAY DIFFRACTIONf_chiral_restr0.0292286
X-RAY DIFFRACTIONf_plane_restr0.0042685
X-RAY DIFFRACTIONf_dihedral_angle_d11.5035458
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 (%)
1.82-1.84070.28192160.22284264448088
1.8407-1.86230.29012320.2214179441188
1.8623-1.8850.26942130.21554295450889
1.885-1.90880.26662030.21064261446489
1.9088-1.93390.25781800.20364196437688
1.9339-1.96030.26112670.19664229449688
1.9603-1.98830.24612360.19134220445688
1.9883-2.01790.24731830.19294154433788
2.0179-2.04940.25111930.19884217441087
2.0494-2.08290.24962420.19674200444288
2.0829-2.11870.24722360.19114194443088
2.1187-2.15720.23692280.19154277450589
2.1572-2.19850.21831940.19314182437688
2.1985-2.24330.2242300.18864193442387
2.2433-2.2920.23672210.19294134435587
2.292-2.34510.24372120.19174226443888
2.3451-2.40360.28132460.19224152439888
2.4036-2.46830.23062240.18144252447689
2.4683-2.54070.20932080.18884207441588
2.5407-2.62240.23522190.18614237445688
2.6224-2.71560.20932200.20054195441588
2.7156-2.82380.22462230.19914188441188
2.8238-2.95160.26782360.20434236447288
2.9516-3.10610.232040.19874274447889
3.1061-3.29920.252140.17264356457090
3.2992-3.55130.18582320.15464441467393
3.5513-3.9040.18492470.14814484473194
3.904-4.45830.16532330.14064490472394
4.4583-5.57740.15952310.14094557478895
5.5774-16.03450.19782290.16584452468193

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