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- PDB-6vc4: Peanut lectin complexed with S-beta-D-Thiogalactopyranosyl beta-D... -

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Basic information

Entry
Database: PDB / ID: 6vc4
TitlePeanut lectin complexed with S-beta-D-Thiogalactopyranosyl beta-D-glucopyranoside derivative (STGD)
ComponentsGalactose-binding lectin
KeywordsSUGAR BINDING PROTEIN / Beta-galactosylamides / Beta-thiogalactosides / Peanut agglutinin / Glycomimetics
Function / homology
Function and homology information


carbohydrate binding / metal ion binding
Similarity search - Function
Legume lectin / Legume lectin, alpha chain, conserved site / Legume lectins alpha-chain signature. / Legume lectins beta-chain signature. / Legume lectin domain / Legume lectin, beta chain, Mn/Ca-binding site / Legume lectin domain / : / Concanavalin A-like lectin/glucanase domain superfamily
Similarity search - Domain/homology
: / Chem-QWG / Galactose-binding lectin
Similarity search - Component
Biological speciesArachis hypogaea (peanut)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsOtero, L.H. / Primo, E.D. / Cagnoni, A.J. / Cano, M.E. / Klinke, S. / Goldbaum, F.A. / Uhrig, M.L.
Funding support Argentina, 2items
OrganizationGrant numberCountry
National Research Council (NRC, Argentina)PICT-2015-0621 Argentina
National Research Council (NRC, Argentina)PICT-2016-1425 Argentina
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2020
Title: Crystal structures of peanut lectin in the presence of synthetic beta-N- and beta-S-galactosides disclose evidence for the recognition of different glycomimetic ligands.
Authors: Cagnoni, A.J. / Primo, E.D. / Klinke, S. / Cano, M.E. / Giordano, W. / Marino, K.V. / Kovensky, J. / Goldbaum, F.A. / Uhrig, M.L. / Otero, L.H.
History
DepositionDec 20, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 28, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 18, 2020Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Oct 11, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _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: Galactose-binding lectin
B: Galactose-binding lectin
C: Galactose-binding lectin
D: Galactose-binding lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,74316
Polymers100,8364
Non-polymers2,90712
Water13,998777
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6330 Å2
ΔGint-30 kcal/mol
Surface area34920 Å2
Unit cell
Length a, b, c (Å)76.067, 124.562, 127.188
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121

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Components

#1: Protein
Galactose-binding lectin / Agglutinin / PNA


Mass: 25208.955 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Arachis hypogaea (peanut) / References: UniProt: P02872
#2: Chemical
ChemComp-QWG / (2R,3R,4S,5R,6S)-2-(hydroxymethyl)-6-{[(2S,3R,4S,5S,6S)-3,4,5-trihydroxy-6-({[(1-{[(2R,3S,4S,5R,6S)-3,4,5-trihydroxy-6-methoxytetrahydro-2H-pyran-2-yl]methyl}-1H-1,2,3-triazol-4-yl)methyl]sulfanyl}methyl)tetrahydro-2H-pyran-2-yl]sulfanyl}tetrahydro-2H-pyran-3,4,5-triol (non-preferred name)


Mass: 631.671 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C22H37N3O14S2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 777 / 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: 2.99 Å3/Da / Density % sol: 58.83 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop
Details: 15% (w/v) PEG 8000, 0.1 sodium citrate, 0.125M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.9801 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Nov 26, 2017
Details: CONVEX PREFOCUSSING MIRROR AND A KIRKPATRICK-BAEZ PAIR OF FOCUSSING MIRRORS
RadiationMonochromator: CRYOGENICALLY COOLED CHANNEL CUT SI[111] CRYSTAL MONOCHROMATOR
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9801 Å / Relative weight: 1
ReflectionResolution: 1.9→62.28 Å / Num. obs: 95802 / % possible obs: 100 % / Redundancy: 11.7 % / CC1/2: 0.997 / Rmerge(I) obs: 0.129 / Rpim(I) all: 0.04 / Rrim(I) all: 0.135 / Net I/σ(I): 11.8
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 11.2 % / Rmerge(I) obs: 1.011 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 4660 / CC1/2: 0.832 / Rpim(I) all: 0.314 / Rrim(I) all: 1.06 / % possible all: 100

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
MxCuBEdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2PEL

2pel


Resolution: 1.9→56.64 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.912 / SU R Cruickshank DPI: 0.149 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.156 / SU Rfree Blow DPI: 0.137 / SU Rfree Cruickshank DPI: 0.133
RfactorNum. reflection% reflectionSelection details
Rfree0.244 4629 4.84 %RANDOM
Rwork0.222 ---
obs0.223 95732 100 %-
Displacement parametersBiso max: 144.11 Å2 / Biso mean: 35.02 Å2 / Biso min: 12.35 Å2
Baniso -1Baniso -2Baniso -3
1-5.488 Å20 Å20 Å2
2--6.3502 Å20 Å2
3----11.8382 Å2
Refinement stepCycle: final / Resolution: 1.9→56.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6972 0 168 778 7918
Biso mean--53.7 41.37 -
Num. residues----928
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d3332SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes176HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1080HARMONIC5
X-RAY DIFFRACTIONt_it7432HARMONIC20
X-RAY DIFFRACTIONt_nbd3SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion1052SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact8929SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d7432HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg10272HARMONIC21.2
X-RAY DIFFRACTIONt_omega_torsion3.91
X-RAY DIFFRACTIONt_other_torsion2.65
LS refinement shellResolution: 1.9→1.95 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3356 322 4.61 %
Rwork0.2996 6660 -
all0.3012 6982 -
obs--99.96 %

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