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- PDB-5xzk: Pholiota squarrosa lectin trimer -

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Basic information

Entry
Database: PDB / ID: 5xzk
TitlePholiota squarrosa lectin trimer
Componentslectin (PhoSL)
KeywordsSUGAR BINDING PROTEIN / Lectin / Trimer / Fucose
Function / homologyLectin (PhoSL)
Function and homology information
Biological speciesPholiota squarrosa (fungus)
MethodSOLUTION NMR / simulated annealing
AuthorsYamasaki, K.
CitationJournal: Sci Rep / Year: 2018
Title: The trimeric solution structure and fucose-binding mechanism of the core fucosylation-specific lectin PhoSL.
Authors: Yamasaki, K. / Yamasaki, T. / Tateno, H.
History
DepositionJul 12, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 6, 2018Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: lectin (PhoSL)
B: lectin (PhoSL)
C: lectin (PhoSL)


Theoretical massNumber of molelcules
Total (without water)13,3233
Polymers13,3233
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, trimer formation was confirmed., cross-linking, trimer formation was confirmed., mass spectrometry, trimer formation was confirmed.
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area3450 Å2
ΔGint-28 kcal/mol
Surface area7350 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 50structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide lectin (PhoSL)


Mass: 4440.958 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) Pholiota squarrosa (fungus) / References: UniProt: A0A384E107*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D NOESY
121isotropic12D TOCSY
131isotropic12D DQF-COSY

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Sample preparation

DetailsType: solution
Contents: 0.3 mM no Pholiota squarrosa lectin (PhoSL), 95% H2O/5% D2O
Details: Concentration value is for peptide, but not for the trimer.
Label: sample / Solvent system: 95% H2O/5% D2O
SampleConc.: 0.3 mM / Component: Pholiota squarrosa lectin (PhoSL) / Isotopic labeling: no
Sample conditionsIonic strength: 0 Not defined / Label: conditions_1 / pH: 7.5 / Pressure: 1 atm / Temperature: 308 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE III HD / Manufacturer: Bruker / Model: AVANCE III HD / Field strength: 900 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CNS1.3BRUNGER, ADAMS, CLORE, GROS, NILGES AND READrefinement
Felix2007structure solution
RefinementMethod: simulated annealing / Software ordinal: 1 / Details: NONCRYSTALLOGRAPHIC SYMMETRY WAS APPLIED
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 20

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