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- PDB-5c9p: Crystal structure of recombinant PLL lectin complexed with L-fuco... -

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Basic information

Entry
Database: PDB / ID: 5c9p
TitleCrystal structure of recombinant PLL lectin complexed with L-fucose from Photorhabdus luminescens at 1.75 A resolution
ComponentsPLL lectin
KeywordsSUGAR BINDING PROTEIN / Lectin / seven-bladed beta-propeller / fucose-specific
Function / homology: / PLL-like beta propeller / Repeat of unknown function (DUF346) / metal ion binding / alpha-L-fucopyranose / Photorhabdus luminescens subsp. laumondii TTO1 complete genome segment 3/17
Function and homology information
Biological speciesPhotorhabdus luminescens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsKumar, A. / Sykorova, P. / Demo, G. / Dobes, P. / Hyrsl, P. / Wimmerova, M.
Funding support Czech Republic, 3items
OrganizationGrant numberCountry
Czech Science Foundation13-25401S Czech Republic
European Regional Development FundCZ.1.05/1.1.00/02.0068 Czech Republic
SYLICACZ.1.05/1.1.00/02.0068 Czech Republic
CitationJournal: J.Biol.Chem. / Year: 2016
Title: A Novel Fucose-binding Lectin from Photorhabdus luminescens (PLL) with an Unusual Heptabladed beta-Propeller Tetrameric Structure.
Authors: Kumar, A. / Sykorova, P. / Demo, G. / Dobes, P. / Hyrsl, P. / Wimmerova, M.
History
DepositionJun 28, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Oct 19, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 2, 2016Group: Database references
Revision 1.2Dec 7, 2016Group: Database references
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / 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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Jan 10, 2024Group: 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
Revision 1.5Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PLL lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,35814
Polymers41,9451
Non-polymers1,41313
Water6,918384
1
A: PLL lectin
hetero molecules

A: PLL lectin
hetero molecules

A: PLL lectin
hetero molecules

A: PLL lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)173,43356
Polymers167,7804
Non-polymers5,65452
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_565x,-y+1,-z1
MethodPISA
Unit cell
Length a, b, c (Å)72.783, 87.717, 158.194
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
SymmetryPoint symmetry: (Schoenflies symbol: C2 (2 fold cyclic))
Components on special symmetry positions
IDModelComponents
11A-227-

CYS

21A-599-

HOH

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Components

#1: Protein PLL lectin


Mass: 41944.949 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Photorhabdus luminescens (bacteria) / Gene: plu0732 / Production host: Escherichia coli (E. coli) / References: UniProt: Q7N8J0
#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.: 3
Source method: isolated from a genetically manipulated source
Formula: C6H12O5
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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 384 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.95 Å3/Da / Density meas: 1009958.938 Mg/m3 / Density % sol: 58.27 % / Description: prism
Crystal growTemperature: 290.15 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 0.1 M Tris-HCl, 2.5 % ethanol, pH 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 6, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 1.75→45.71 Å / Num. obs: 51368 / % possible obs: 100 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 14.1
Reflection shellResolution: 1.75→1.84 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.462 / Mean I/σ(I) obs: 3.4 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5C9O

5c9o


Resolution: 1.75→39.1 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.957 / SU B: 1.786 / SU ML: 0.055 / Cross valid method: THROUGHOUT / ESU R: 0.076 / ESU R Free: 0.083 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18111 2608 5.1 %RANDOM
Rwork0.1417 ---
obs0.14363 48756 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.931 Å2
Baniso -1Baniso -2Baniso -3
1-1.82 Å20 Å2-0 Å2
2---0.8 Å20 Å2
3----1.01 Å2
Refinement stepCycle: 1 / Resolution: 1.75→39.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2750 0 93 384 3227
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0192959
X-RAY DIFFRACTIONr_bond_other_d0.0030.022665
X-RAY DIFFRACTIONr_angle_refined_deg2.1241.9014064
X-RAY DIFFRACTIONr_angle_other_deg1.17636105
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.1585371
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.26124.318132
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.99615411
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.6981514
X-RAY DIFFRACTIONr_chiral_restr0.1540.2467
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.023379
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02741
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.1641.6821433
X-RAY DIFFRACTIONr_mcbond_other2.1451.681432
X-RAY DIFFRACTIONr_mcangle_it3.0642.511794
X-RAY DIFFRACTIONr_mcangle_other3.0662.5121795
X-RAY DIFFRACTIONr_scbond_it3.0921.9181525
X-RAY DIFFRACTIONr_scbond_other3.0851.9191525
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.4272.7882262
X-RAY DIFFRACTIONr_long_range_B_refined6.38715.43696
X-RAY DIFFRACTIONr_long_range_B_other5.95614.563474
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.75→1.795 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.233 190 -
Rwork0.197 3548 -
obs--99.84 %

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