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- PDB-4a6s: Structure of the PAIL lectin from Pseudomonas aeruginosa in compl... -

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Basic information

Entry
Database: PDB / ID: 4a6s
TitleStructure of the PAIL lectin from Pseudomonas aeruginosa in complex with 2-Naphtyl-1-thio-beta-D-galactopyranoside
ComponentsPA-I GALACTOPHILIC LECTIN
KeywordsSUGAR BINDING PROTEIN / SUGAR-BINDING PROTEIN / GLYCOMIMETIC
Function / homology
Function and homology information


heterophilic cell-cell adhesion / 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
naphthalen-2-yl 1-thio-beta-D-galactopyranoside / PA-I galactophilic lectin
Similarity search - Component
Biological speciesPSEUDOMONAS AERUGINOSA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsRodrigue, J. / Ganne, G. / Blanchard, B. / Saucier, C. / Giguere, D. / Chiao, T.S. / Varrot, A. / Imberty, A. / Roy, R.
CitationJournal: Org.Biomol.Chem. / Year: 2013
Title: Aromatic Thioglycoside Inhibitors Against the Virulence Factor Leca from Pseudomonas Aeruginosa.
Authors: Rodrigue, J. / Ganne, G. / Blanchard, B. / Saucier, C. / Giguere, D. / Shiao, T.C. / Varrot, A. / Imberty, A. / Roy, R.
History
DepositionNov 8, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 17, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 14, 2012Group: Atomic model / Other
Revision 1.2Oct 2, 2013Group: Database references
Revision 1.3Oct 9, 2013Group: Database references
Revision 1.4Jul 29, 2020Group: Derived calculations / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_database_status / pdbx_entity_nonpoly / 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 / _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.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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Dec 20, 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 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.

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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)52,53012
Polymers51,0814
Non-polymers1,4508
Water4,216234
1
A: PA-I GALACTOPHILIC LECTIN
B: PA-I GALACTOPHILIC LECTIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,2656
Polymers25,5402
Non-polymers7254
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2030 Å2
ΔGint-6.4 kcal/mol
Surface area10630 Å2
MethodPISA
2
C: PA-I GALACTOPHILIC LECTIN
D: PA-I GALACTOPHILIC LECTIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,2656
Polymers25,5402
Non-polymers7254
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2020 Å2
ΔGint-6.5 kcal/mol
Surface area10660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.334, 54.334, 390.501
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11B-2039-

HOH

21B-2057-

HOH

Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.6431, 0.1598, 0.7489), (0.1621, -0.9274, 0.3371), (0.7484, 0.3385, 0.5705)-40.8, 30.8, 12.84
2given(0.1227, 0.6867, -0.7165), (0.6878, -0.5793, -0.4375), (-0.7155, -0.4391, -0.5434)1.796, 52.92, 53.56
3given(-0.5004, -0.862, -0.08103), (-0.8655, 0.4956, 0.0734), (-0.0231, 1.269, -0.994)8.54, 1.269, 62.31

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Components

#1: Protein
PA-I GALACTOPHILIC LECTIN / PA-IL / GALACTOSE-BINDING LECTIN


Mass: 12770.137 Da / Num. of mol.: 4 / Fragment: RESIDUES 2-122
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PSEUDOMONAS AERUGINOSA (bacteria) / Strain: PAO1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q05097
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Sugar
ChemComp-GS9 / naphthalen-2-yl 1-thio-beta-D-galactopyranoside / naphthalen-2-yl 1-thio-beta-D-galactoside / naphthalen-2-yl 1-thio-D-galactoside / naphthalen-2-yl 1-thio-galactoside


Type: D-saccharide / Mass: 322.376 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C16H18O5S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 234 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsALL NUMBERING SHIFTED BY 1 SINCE N-TERMINAL METHIONINE IS CLEAVED.

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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: 3.06 Å3/Da / Density % sol: 59.78 % / Description: NONE
Crystal growpH: 4.5
Details: 0.8 M LISO4, 100 MM SODIUM ACETATE PH 4.5, 25% GLYCEROL (ADDED FOR CRYPROTECTION).

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.97623
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 25, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97623 Å / Relative weight: 1
ReflectionResolution: 2.15→40 Å / Num. obs: 37963 / % possible obs: 99.5 % / Observed criterion σ(I): 2 / Redundancy: 3.5 % / Biso Wilson estimate: 40 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 14.4
Reflection shellResolution: 2.15→2.27 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 2.3 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1OKO

1oko


Resolution: 2.15→38.13 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.93 / SU B: 14.076 / SU ML: 0.174 / Cross valid method: THROUGHOUT / ESU R: 0.207 / ESU R Free: 0.188 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.25881 1888 5 %RANDOM
Rwork0.21437 ---
obs0.21657 35959 99.26 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 44.949 Å2
Baniso -1Baniso -2Baniso -3
1-2.35 Å21.17 Å20 Å2
2--2.35 Å20 Å2
3----3.52 Å2
Refinement stepCycle: LAST / Resolution: 2.15→38.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3604 0 92 234 3930
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.023799
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6571.9495202
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4645482
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.55125.854164
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.55415520
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.275158
X-RAY DIFFRACTIONr_chiral_restr0.1020.2565
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212972
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2230.21969
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3250.22571
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1560.2193
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.1270.215
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2260.227
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2610.25
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
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: 2.15→2.206 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.363 131 -
Rwork0.328 2325 -
obs--99.96 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.17050.26811.82331.42520.11934.590.23230.1123-0.11460.1805-0.0137-0.03820.07720.0688-0.21860.58360.0597-0.04560.0218-0.05810.25475.522614.863650.9895
22.22670.76780.9231.96390.94574.23510.28120.05340.28510.145-0.07220.0457-0.2622-0.0547-0.2090.67150.08330.16160.024-0.01630.2917-3.761535.086651.1015
31.90660.19531.79752.14511.13884.5429-0.18470.06820.11210.00950.27830.4007-0.2214-0.4389-0.09360.37110.06140.07350.4510.17940.3768-23.827225.796115.3765
41.72180.22791.53681.24760.94784.47660.03610.1979-0.09550.06030.347-0.02910.25740.0431-0.38310.39230.0083-0.0480.3635-0.02940.2743-11.17737.597613.1143
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 151
2X-RAY DIFFRACTION2B1 - 151
3X-RAY DIFFRACTION3C1 - 151
4X-RAY DIFFRACTION4D1 - 151

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