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- PDB-6vto: Crystal structure of human Galectin-7 in complex with 4-O-beta-D-... -

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Basic information

Entry
Database: PDB / ID: 6vto
TitleCrystal structure of human Galectin-7 in complex with 4-O-beta-D-Galactopyranosyl-D-glucose
ComponentsGalectin-7
KeywordsSUGAR BINDING PROTEIN / Human Galectin-7 / lactose-furanose
Function / homology
Function and homology information


heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / carbohydrate binding / apoptotic process / extracellular space / extracellular exosome / nucleus / cytoplasm
Similarity search - Function
Galectin-like / Galactoside-binding lectin / Galectin / Galectin, carbohydrate recognition domain / Galactoside-binding lectin / Galactoside-binding lectin (galectin) domain profile. / Concanavalin A-like lectin/glucanase domain superfamily
Similarity search - Domain/homology
Chem-LBL / Galectin-7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.69 Å
AuthorsPham, N.T.H. / Calmettes, C. / Doucet, N.
Funding support Canada, United States, 6items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada)RGPIN 2016-05557 Canada
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM105978 United States
Fonds de Recherche du Quebec - Sante (FRQS)Research Scholar Senior Career Award (281993) Canada
Fonds de Recherche du Quebec - Sante (FRQS)Junior 1 (251848) Canada
Natural Sciences and Engineering Research Council (NSERC, Canada)RGPIN-2017-06091 Canada
Fonds de Recherche du Quebec - Sante (FRQS)Doctoral Training scholarship (287239) Canada
CitationJournal: J.Biol.Chem. / Year: 2021
Title: Perturbing dimer interactions and allosteric communication modulates the immunosuppressive activity of human galectin-7.
Authors: Pham, N.T.H. / Letourneau, M. / Fortier, M. / Begin, G. / Al-Abdul-Wahid, M.S. / Pucci, F. / Folch, B. / Rooman, M. / Chatenet, D. / St-Pierre, Y. / Lague, P. / Calmettes, C. / Doucet, N.
History
DepositionFeb 13, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 25, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 17, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 24, 2021Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.3Oct 11, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Galectin-7
B: Galectin-7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,6164
Polymers29,9322
Non-polymers6852
Water5,639313
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)30.520, 77.240, 111.440
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Galectin-7 / Gal-7 / HKL-14 / PI7 / p53-induced gene 1 protein


Mass: 14965.850 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LGALS7, PIG1, LGALS7B / Plasmid: pET22b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P47929
#2: Chemical ChemComp-LBL / (2~{R},3~{R},4~{R},5~{R})-4-[(2~{S},3~{R},4~{S},5~{R},6~{R})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-2,3,5, 6-tetrakis(oxidanyl)hexanal / 4-O-beta-D-Galactopyranosyl-D-glucose


Mass: 342.296 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H22O11 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 313 / 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: 2.19 Å3/Da / Density % sol: 43.94 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.1 M Sodium Chloride, 0.1 M Tris pH 8, 20 % PEG3350, 5 % Glycerol
Temp details: Room temperature

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08B1-1 / Wavelength: 1.0332 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Feb 18, 2019 / Details: 16 tiled fiber-optic tapers
RadiationMonochromator: KOHZU double crystal monochromator (DCM) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.69→45.19 Å / Num. obs: 30152 / % possible obs: 99.11 % / Redundancy: 6.85 % / Biso Wilson estimate: 30.173 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.086 / Rrim(I) all: 0.093 / Net I/σ(I): 15.7 / Num. measured all: 206559
Reflection shellResolution: 1.69→1.75 Å / Redundancy: 7.17 % / Rmerge(I) obs: 0.836 / Mean I/σ(I) obs: 3 / Num. measured obs: 21014 / Num. unique obs: 2930 / CC1/2: 0.839 / Rrim(I) all: 0.901 / % possible all: 99.25

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation5.99 Å45.19 Å
Translation5.99 Å45.19 Å

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Processing

Software
NameVersionClassification
PHENIX1.17.1-3660refinement
XDSdata reduction
XSCALEdata scaling
PHASER2.7.12phasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4gal

4gal


Resolution: 1.69→45.19 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.29 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2149 1185 3.93 %
Rwork0.1832 28959 -
obs0.1845 30144 99.09 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 95.98 Å2 / Biso mean: 21.037 Å2 / Biso min: 5.25 Å2
Refinement stepCycle: final / Resolution: 1.69→45.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2104 0 90 313 2507
Biso mean--26.84 29.58 -
Num. residues----268
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.69-1.770.32651450.27283545369099
1.77-1.860.25661450.21063525367099
1.86-1.980.25461430.2283522366598
1.98-2.130.24211470.18863585373299
2.13-2.340.22481480.19623607375599
2.34-2.680.24081480.176736263774100
2.68-3.380.17691510.167236943845100
3.38-45.190.18461580.160838554013100

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