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- PDB-4lk6: Crystal Structure of Pseudomonas aeruginosa Lectin LecA Complexed... -

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Basic information

Entry
Database: PDB / ID: 4lk6
TitleCrystal Structure of Pseudomonas aeruginosa Lectin LecA Complexed with Chlorophenol Red-b-D-galactopyranoside at 2.86 A Resolution
ComponentsPA-I galactophilic lectin
KeywordsSUGAR BINDING PROTEIN / Lectin Fold / Galactose
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
beta-D-galactopyranose / Chem-LRD / PA-I galactophilic lectin
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.859 Å
AuthorsKadam, R.U. / Stocker, A. / Reymond, J.L.
CitationJournal: Acs Chem.Biol. / Year: 2013
Title: CH-pi "T-Shape" Interaction with Histidine Explains Binding of Aromatic Galactosides to Pseudomonas aeruginosa Lectin LecA
Authors: Kadam, R.U. / Garg, D. / Schwartz, J. / Visini, R. / Sattler, M. / Stocker, A. / Darbre, T. / Reymond, J.L.
History
DepositionJul 6, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 30, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 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_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.pdbx_leaving_atom_flag / _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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2Nov 8, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)160,96448
Polymers153,24212
Non-polymers7,72236
Water5,080282
1
A: PA-I galactophilic lectin
B: PA-I galactophilic lectin
F: PA-I galactophilic lectin
G: PA-I galactophilic lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,65516
Polymers51,0814
Non-polymers2,57412
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: PA-I galactophilic lectin
I: PA-I galactophilic lectin
J: PA-I galactophilic lectin
K: PA-I galactophilic lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,65516
Polymers51,0814
Non-polymers2,57412
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
D: PA-I galactophilic lectin
E: PA-I galactophilic lectin
H: PA-I galactophilic lectin
L: PA-I galactophilic lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,65516
Polymers51,0814
Non-polymers2,57412
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)89.068, 150.829, 185.817
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
PA-I galactophilic lectin


Mass: 12770.137 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228 / Gene: lecA, pa1L, PA2570 / Plasmid: PET25PAIL / 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.: 12 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-LRD / 2-[(E)-(3-chloro-4-hydroxyphenyl)(3-chloro-4-oxocyclohexa-2,5-dien-1-ylidene)methyl]benzenesulfonic acid / Chlorophenol Red / Chlorophenol red


Mass: 423.267 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C19H12Cl2O5S
#4: Sugar
ChemComp-GAL / beta-D-galactopyranose / beta-D-galactose / D-galactose / galactose / 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
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 282 / 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: 4.07 Å3/Da / Density % sol: 69.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 2.4M Sodium malonate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 12, 2011
RadiationMonochromator: Bartels Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.859→48.927 Å / Num. all: 109598 / Num. obs: 109598 / % possible obs: 97.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3
Reflection shellHighest resolution: 2.86 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.72 / Mean I/σ(I) obs: 2.19 / Num. unique all: 109598 / % possible all: 90.2

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Processing

Software
NameVersionClassification
SLSPSI- X06DAdata collection
PHASERphasing
PHENIX(phenix.refine: 1.6.4_486)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ZYE

3zye


Resolution: 2.859→48.92 Å / SU ML: 0.4 / σ(F): 1.99 / Phase error: 30.3 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2708 5448 4.98 %RANDOM
Rwork0.2351 ---
all0.2369 109304 --
obs0.2369 109304 97.73 %-
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 30.543 Å2 / ksol: 0.332 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--18.8722 Å2-0 Å20 Å2
2---2.9695 Å20 Å2
3---21.8417 Å2
Refinement stepCycle: LAST / Resolution: 2.859→48.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10812 0 468 282 11562
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00111580
X-RAY DIFFRACTIONf_angle_d0.5115900
X-RAY DIFFRACTIONf_dihedral_angle_d16.6214272
X-RAY DIFFRACTIONf_chiral_restr0.0411704
X-RAY DIFFRACTIONf_plane_restr0.0022064
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.859-2.96120.39134700.3501897684
2.9612-3.07970.35585620.318610622100
3.0797-3.21990.34345350.289510579100
3.2199-3.38960.29775570.253410574100
3.3896-3.60190.27645510.24261055599
3.6019-3.87990.29025510.24041047298
3.8799-4.27010.24395560.21131048299
4.2701-4.88750.22125550.190610565100
4.8875-6.15590.25475530.21021051599
6.1559-48.93450.23675580.21731051699

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