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- PDB-7psy: X-ray crystal structure of perdeuterated LecB lectin in complex w... -

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Basic information

Entry
Database: PDB / ID: 7psy
TitleX-ray crystal structure of perdeuterated LecB lectin in complex with perdeuterated fucose
ComponentsFucose-binding lectin
KeywordsSUGAR BINDING PROTEIN / lectin / complex
Function / homologyLectin, sugar-binding / Calcium-mediated lectin / Calcium-mediated lectin superfamily / Fucose-binding lectin II (PA-IIL) / carbohydrate binding / alpha-L-fucopyranose / Fucose-binding lectin
Function and homology information
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.9 Å
AuthorsGajdos, L. / Blakeley, M.P. / Haertlein, M. / Forsyth, T.V. / Devos, J.M. / Imberty, A.
Funding support France, 1items
OrganizationGrant numberCountry
Institut Laue-Langevin France
CitationJournal: Nat Commun / Year: 2022
Title: Neutron crystallography reveals mechanisms used by Pseudomonas aeruginosa for host-cell binding.
Authors: Gajdos, L. / Blakeley, M.P. / Haertlein, M. / Forsyth, V.T. / Devos, J.M. / Imberty, A.
History
DepositionSep 24, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 12, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 26, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fucose-binding lectin
B: Fucose-binding lectin
C: Fucose-binding lectin
D: Fucose-binding lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,63318
Polymers47,4644
Non-polymers1,16914
Water14,394799
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10520 Å2
ΔGint-155 kcal/mol
Surface area15360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.600, 72.989, 55.190
Angle α, β, γ (deg.)90.000, 94.578, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein
Fucose-binding lectin / Fucose-binding lectin II (PA-IIL) / Fucose-binding lectin PA-IIL


Mass: 11865.905 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria)
Gene: lecB, C0044_25260, CAZ10_21840, DT376_00595, DY979_15445, ECC04_10105, EFK27_13700, EGV95_09240, EGY23_15550, IPC669_23070, PA5486_01888, PAERUG_E15_London_28_01_14_00983, PAMH19_1713, RW109_RW109_02453
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A069Q9V4
#2: Sugar
ChemComp-FUC / alpha-L-fucopyranose / alpha-L-fucose / 6-deoxy-alpha-L-galactopyranose / L-fucose / fucose


Type: L-saccharide, alpha linking / Mass: 164.156 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H12O5 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
LFucpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-L-fucopyranoseCOMMON NAMEGMML 1.0
a-L-FucpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
FucSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 799 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.22 Å3/Da / Density % sol: 44.72 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Tris/DCl, pD 7.1, 20% (w/v) PEG 4000

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97856 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 29, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 0.9→36.5 Å / Num. obs: 270061 / % possible obs: 87.6 % / Redundancy: 6.1 % / Biso Wilson estimate: 8.83 Å2 / CC1/2: 1 / Net I/σ(I): 16.3
Reflection shellResolution: 0.9→0.92 Å / Num. unique obs: 5821 / CC1/2: 0.63

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1GZT

1gzt


Resolution: 0.9→36.53 Å / SU ML: 0.0894 / Cross valid method: FREE R-VALUE / σ(F): 1.92 / Phase error: 16.3494
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1313 25913 4.92 %
Rwork0.1158 500935 -
obs0.1166 526848 86.17 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 13.89 Å2
Refinement stepCycle: LAST / Resolution: 0.9→36.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3308 0 62 774 4144
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083700
X-RAY DIFFRACTIONf_angle_d1.1075131
X-RAY DIFFRACTIONf_chiral_restr0.0917638
X-RAY DIFFRACTIONf_plane_restr0.0075702
X-RAY DIFFRACTIONf_dihedral_angle_d3.41882350
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
0.9-0.910.35341070.39232526X-RAY DIFFRACTION12.91
0.91-0.920.39642410.38514464X-RAY DIFFRACTION23.17
0.92-0.930.37483420.38847076X-RAY DIFFRACTION36.52
0.93-0.940.38865080.37289782X-RAY DIFFRACTION50.46
0.94-0.950.36456580.350812297X-RAY DIFFRACTION63.2
0.95-0.970.34817780.332514651X-RAY DIFFRACTION76.13
0.97-0.980.30878620.303116715X-RAY DIFFRACTION86.32
0.98-10.26899280.276817601X-RAY DIFFRACTION90.78
1-1.010.24959270.255817980X-RAY DIFFRACTION92.74
1.01-1.030.25269080.241118294X-RAY DIFFRACTION94.19
1.03-1.050.23889090.219618443X-RAY DIFFRACTION94.73
1.05-1.060.20059060.199418365X-RAY DIFFRACTION94.86
1.06-1.080.20610280.180618414X-RAY DIFFRACTION95.07
1.08-1.110.177910000.165118425X-RAY DIFFRACTION95.4
1.11-1.130.15129870.141518468X-RAY DIFFRACTION95.5
1.13-1.160.1249740.118818679X-RAY DIFFRACTION96.55
1.16-1.190.12969920.103318789X-RAY DIFFRACTION97.03
1.19-1.220.11919760.096418997X-RAY DIFFRACTION97.66
1.22-1.250.11148590.092719144X-RAY DIFFRACTION98.25
1.25-1.290.10369510.092719056X-RAY DIFFRACTION98.45
1.29-1.340.11298870.088219254X-RAY DIFFRACTION98.79
1.34-1.390.1099590.089119193X-RAY DIFFRACTION99
1.39-1.460.102310070.085319278X-RAY DIFFRACTION99.18
1.46-1.540.10079940.084819273X-RAY DIFFRACTION99.66
1.54-1.630.103910060.083219390X-RAY DIFFRACTION99.92
1.63-1.760.10439900.090419354X-RAY DIFFRACTION99.99
1.76-1.930.107111250.091319229X-RAY DIFFRACTION99.97
1.93-2.210.10439370.092719478X-RAY DIFFRACTION99.96
2.21-2.790.108810120.101919341X-RAY DIFFRACTION99.95
2.79-36.530.135511550.113718979X-RAY DIFFRACTION98.78

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