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

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Basic information

Entry
Database: PDB / ID: 4ljh
TitleCrystal Structure of Pseudomonas aeruginosa Lectin LecA Complexed with 1-Methyl-3-indolyl-b-D-galactopyranoside at 1.45 A Resolution
ComponentsPA-I galactophilic lectin
KeywordsSUGAR BINDING PROTEIN / ADHESIN / GLYCOSPHINGOLIPID-ANTIGEN / GALACTOSE-SPECIFIC / GALACTOSIDES / lectin fold / Galactose / Glycosylation / outer membrane
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
beta-D-galactopyranose / 1-methyl-1H-indol-3-ol / PA-I galactophilic lectin
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 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 4, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 30, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software
Revision 1.2Jul 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 1.3Nov 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,07516
Polymers51,6054
Non-polymers1,47012
Water12,106672
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.6, 68.2, 159.4
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 / PA-IL / Galactose-binding lectin


Mass: 12901.333 Da / Num. of mol.: 4
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 / 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-MHD / 1-methyl-1H-indol-3-ol


Mass: 147.174 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C9H9NO
#4: Sugar
ChemComp-GAL / beta-D-galactopyranose / beta-D-galactose / D-galactose / galactose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 4
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


Mass: 18.015 Da / Num. of mol.: 672 / 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: 2.61 Å3/Da / Density % sol: 52.91 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 0.1M Sodium acetate trihydrate, 3.0M Sodium chloride, pH 4.5), 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: 1.45→47.404 Å / Num. obs: 181878 / % possible obs: 98.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3
Reflection shellHighest resolution: 1.45 Å / % possible all: 98.1

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Processing

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

3zye


Resolution: 1.45→47.4 Å / SU ML: 0.2 / σ(F): 1.99 / Phase error: 24.84 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2112 9110 5.01 %RANDOM
Rwork0.1895 ---
all0.1906 181878 --
obs0.1906 181709 98.06 %-
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 45.013 Å2 / ksol: 0.4 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--7.1595 Å20 Å2-0 Å2
2--15.0876 Å2-0 Å2
3----7.928 Å2
Refinement stepCycle: LAST / Resolution: 1.45→47.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3604 0 92 672 4368
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053792
X-RAY DIFFRACTIONf_angle_d1.0095196
X-RAY DIFFRACTIONf_dihedral_angle_d24.8951352
X-RAY DIFFRACTIONf_chiral_restr0.068564
X-RAY DIFFRACTIONf_plane_restr0.005680
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 (%)
1.4504-1.50230.35738540.34291613892
1.5023-1.56240.33468990.30581703597
1.5624-1.63350.28589200.2731731699
1.6335-1.71970.25289140.23621747599
1.7197-1.82740.25249290.198417510100
1.8274-1.96850.19569270.172417531100
1.9685-2.16660.18339320.158717524100
2.1666-2.48010.20039170.17241743699
2.4801-3.12460.21529020.17741741699
3.1246-47.42940.16999160.16391721898
Refinement TLS params.Method: refined / Origin x: 25.082 Å / Origin y: 24.4207 Å / Origin z: 19.614 Å
111213212223313233
T0.1302 Å20.0062 Å20.0045 Å2-0.1321 Å2-0.02 Å2--0.1179 Å2
L0.2314 °20.0445 °20.0919 °2-0.0628 °20.0346 °2--0.0773 °2
S0.005 Å °-0.0488 Å °0.0168 Å °0.0097 Å °-0.0015 Å °-0.0029 Å °-0.0064 Å °0.0077 Å °-0 Å °
Refinement TLS groupSelection details: ALL

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