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- PDB-6vc3: Peanut lectin complexed with S-beta-D-thiogalactopyranosyl 6-deox... -

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Basic information

Entry
Database: PDB / ID: 6vc3
TitlePeanut lectin complexed with S-beta-D-thiogalactopyranosyl 6-deoxy-6-S-propynyl-beta-D-glucopyranoside (STG)
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 domain / Legume lectin, beta chain, Mn/Ca-binding site / : / Concanavalin A-like lectin/glucanase domain superfamily
Similarity search - Domain/homology
: / Chem-QWJ / Galactose-binding lectin
Similarity search - Component
Biological speciesArachis hypogaea (peanut)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 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)102,45315
Polymers100,8364
Non-polymers1,61711
Water9,980554
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7380 Å2
ΔGint-107 kcal/mol
Surface area33680 Å2
Unit cell
Length a, b, c (Å)76.190, 125.418, 128.112
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-QWJ / 6-S-(prop-2-yn-1-yl)-6-thio-beta-D-glucopyranosyl 1-thio-beta-D-galactopyranoside


Mass: 412.476 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C15H24O9S2 / 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.: 554 / 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: 3.04 Å3/Da / Density % sol: 59.47 %
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: 1.95→49.03 Å / Num. obs: 82675 / % possible obs: 92.8 % / Redundancy: 9.3 % / CC1/2: 0.997 / Rmerge(I) obs: 0.12 / Rpim(I) all: 0.039 / Rrim(I) all: 0.127 / Net I/σ(I): 10.7
Reflection shellResolution: 1.95→1.99 Å / Redundancy: 9.6 % / Rmerge(I) obs: 0.802 / Mean I/σ(I) obs: 2 / Num. unique obs: 4496 / CC1/2: 0.757 / Rpim(I) all: 0.254 / Rrim(I) all: 0.846 / % possible all: 95.7

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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: 1.95→49.03 Å / Cor.coef. Fo:Fc: 0.896 / Cor.coef. Fo:Fc free: 0.89 / SU R Cruickshank DPI: 0.205 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.21 / SU Rfree Blow DPI: 0.174 / SU Rfree Cruickshank DPI: 0.172
RfactorNum. reflection% reflectionSelection details
Rfree0.283 4228 5.11 %RANDOM
Rwork0.267 ---
obs0.268 82672 91.8 %-
Displacement parametersBiso max: 175.73 Å2 / Biso mean: 37.57 Å2 / Biso min: 10.99 Å2
Baniso -1Baniso -2Baniso -3
1-10.0552 Å20 Å20 Å2
2--4.0784 Å20 Å2
3----14.1336 Å2
Refinement stepCycle: final / Resolution: 1.95→49.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6972 0 77 555 7604
Biso mean--78.74 35.53 -
Num. residues----928
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d3253SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes176HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1047HARMONIC5
X-RAY DIFFRACTIONt_it7269HARMONIC20
X-RAY DIFFRACTIONt_nbd4SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion1022SEMIHARMONIC5
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_contact8442SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d7269HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg9977HARMONIC21.19
X-RAY DIFFRACTIONt_omega_torsion3.52
X-RAY DIFFRACTIONt_other_torsion2.67
LS refinement shellResolution: 1.95→2 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3716 304 4.89 %
Rwork0.3605 5917 -
all0.361 6221 -
obs--95.05 %

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