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- PDB-6vav: Peanut lectin complexed with divalent N-beta-D-galactopyranosyl-L... -

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Basic information

Entry
Database: PDB / ID: 6vav
TitlePeanut lectin complexed with divalent N-beta-D-galactopyranosyl-L-succinamoyl derivative (diNGS)
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-QTY / Galactose-binding lectin
Similarity search - Component
Biological speciesArachis hypogaea (peanut)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsOtero, L.H. / Primo, E.D. / Cagnoni, A.J. / 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 18, 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.journal_volume / _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)104,43614
Polymers100,8364
Non-polymers3,60010
Water18,3931021
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)75.760, 124.640, 128.375
Angle α, β, γ (deg.)90.00, 90.00, 90.00
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-QTY / N-[[1-[(3S,3aR,6S,6aR)-6-[4-[[[4-[[(2R,3R,4S,5R,6R)-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]amino]-4-oxidanylidene-butanoyl]amino]methyl]-1,2,3-triazol-1-yl]-2,3,3a,5,6,6a-hexahydrofuro[3,2-b]furan-3-yl]-1,2,3-triazol-4-yl]methyl]-N'-[(2R,3R,4S,5R,6R)-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]butanediamide


Mass: 828.781 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C32H48N10O16
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mn
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1021 / 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: 3.01 Å3/Da / Density % sol: 59.07 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop
Details: 15% (w/v) PEG 8000, 0.1M sodium citrate, 0.1M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9786 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 18, 2018 / Details: KIRKPATRICK-BAEZ PAIR OF BIMORPH MIRRORS
RadiationMonochromator: CHANNEL CUT CRYOGENICALLY COOLED CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 1.85→48.97 Å / Num. obs: 104262 / % possible obs: 100 % / Redundancy: 7.4 % / Rmerge(I) obs: 0.083 / Net I/σ(I): 14.4
Reflection shellResolution: 1.85→1.88 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.814 / Mean I/σ(I) obs: 2.2 / % 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: 1.85→27.09 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.931 / SU R Cruickshank DPI: 0.13 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.139 / SU Rfree Blow DPI: 0.122 / SU Rfree Cruickshank DPI: 0.117
RfactorNum. reflection% reflectionSelection details
Rfree0.225 5073 4.87 %RANDOM
Rwork0.205 ---
obs0.206 104167 100 %-
Displacement parametersBiso mean: 33.1 Å2
Baniso -1Baniso -2Baniso -3
1-2.036 Å20 Å20 Å2
2--5.3559 Å20 Å2
3----7.3919 Å2
Refinement stepCycle: LAST / Resolution: 1.85→27.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6972 0 240 1021 8233
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.017560HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.1810512HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d3376SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes176HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1148HARMONIC5
X-RAY DIFFRACTIONt_it7560HARMONIC20
X-RAY DIFFRACTIONt_nbd14SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion4.12
X-RAY DIFFRACTIONt_other_torsion2.63
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1048SEMIHARMONIC5
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_contact9321SEMIHARMONIC4
LS refinement shellResolution: 1.85→1.9 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2865 401 5.29 %
Rwork0.2723 7184 -
all0.2731 7585 -
obs--99.97 %

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