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

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Basic information

Entry
Database: PDB / ID: 4lkd
TitleCrystal Structure of Pseudomonas aeruginosa Lectin LecA Complexed with GalA-QRS at 2.31 A Resolution
Components
  • PA-I galactophilic lectin
  • peptide QRSA
KeywordsSUGAR BINDING PROTEIN/INHIBITOR / Lectin Fold / Sugar Binding Protein / Galactose / SUGAR BINDING PROTEIN-INHIBITOR complex
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 / P-HYDROXYBENZOIC ACID / PA-I galactophilic lectin
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.307 Å
AuthorsKadam, R.U. / Stocker, A. / Reymond, J.-L.
CitationJournal: Chemistry / Year: 2013
Title: Structure-Based Optimization of the Terminal Tripeptide in Glycopeptide Dendrimer Inhibitors of Pseudomonas aeruginosa Biofilms Targeting LecA.
Authors: Kadam, R.U. / Bergmann, M. / Garg, D. / Gabrieli, G. / Stocker, A. / Darbre, T. / Reymond, J.-L.
History
DepositionJul 7, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 18, 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_label_asym_id
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: peptide QRSA
J: peptide QRSA
K: peptide QRSA
L: peptide QRSA
M: peptide QRSA
N: peptide QRSA
O: peptide QRSA
P: peptide QRSA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,72040
Polymers105,85316
Non-polymers2,86724
Water20,4651136
1
A: PA-I galactophilic lectin
C: PA-I galactophilic lectin
D: PA-I galactophilic lectin
E: PA-I galactophilic lectin
I: peptide QRSA
K: peptide QRSA
L: peptide QRSA
M: peptide QRSA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,36020
Polymers52,9278
Non-polymers1,43312
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: PA-I galactophilic lectin
F: PA-I galactophilic lectin
G: PA-I galactophilic lectin
H: PA-I galactophilic lectin
J: peptide QRSA
N: peptide QRSA
O: peptide QRSA
P: peptide QRSA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,36020
Polymers52,9278
Non-polymers1,43312
Water1267
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)159.216, 149.239, 87.018
Angle α, β, γ (deg.)90.00, 110.96, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11C-370-

HOH

21C-408-

HOH

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Components

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Protein / Protein/peptide / Sugars , 3 types, 24 molecules ABCDEFGHIJKLMNOP

#1: Protein
PA-I galactophilic lectin


Mass: 12770.137 Da / Num. of mol.: 8
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: Protein/peptide
peptide QRSA


Mass: 461.493 Da / Num. of mol.: 8 / Source method: obtained synthetically / Details: The peptide was chemically synthesized.
#3: Sugar
ChemComp-GAL / beta-D-galactopyranose / Galactose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 8
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

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Non-polymers , 3 types, 1152 molecules

#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca
#5: Chemical
ChemComp-PHB / P-HYDROXYBENZOIC ACID / 4-Hydroxybenzoic acid


Mass: 138.121 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C7H6O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1136 / 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: 4.56 Å3/Da / Density % sol: 73.03 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 1.5M Lithium sulfate monohydrate, 0.1M Tris pH 8.5 , 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: May 14, 2011
RadiationMonochromator: Bartels Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.307→48.461 Å / Num. all: 81750 / Num. obs: 81750 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 2.4 % / Biso Wilson estimate: 33.6 Å2 / Net I/σ(I): 9.1
Reflection shellResolution: 2.31→2.45 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.789 / Mean I/σ(I) obs: 2 / Num. unique all: 81750 / % possible all: 92.9

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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 / Resolution: 2.307→48.46 Å / SU ML: 0.36 / σ(F): 1.99 / Phase error: 24.24 / Stereochemistry target values: ML
Details: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS
RfactorNum. reflection% reflectionSelection details
Rfree0.2474 7657 5 %RANDOM
Rwork0.2146 ---
all0.2162 81750 --
obs0.2162 81750 92.94 %-
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 36.532 Å2 / ksol: 0.361 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-7.2943 Å2-0 Å2-4.0964 Å2
2---9.7047 Å2-0 Å2
3---2.4104 Å2
Refinement stepCycle: LAST / Resolution: 2.307→48.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7377 0 168 1136 8681
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0027729
X-RAY DIFFRACTIONf_angle_d0.67210560
X-RAY DIFFRACTIONf_dihedral_angle_d10.1122788
X-RAY DIFFRACTIONf_chiral_restr0.0341147
X-RAY DIFFRACTIONf_plane_restr0.0181395
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 (%)
2.3071-2.38950.34067190.29831372788
2.3895-2.48520.30297730.27391471594
2.4852-2.59830.29597760.26281460594
2.5983-2.73530.27737750.24521466794
2.7353-2.90660.27837760.2371458594
2.9066-3.1310.24097700.21331470194
3.131-3.4460.23137760.19931461494
3.446-3.94450.22447450.18351462193
3.9445-4.96880.19257760.16881459493
4.9688-48.47140.25227710.21881453393

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