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- PDB-6vtq: Crystal structure of G16C human Galectin-7 mutant in complex with... -

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Basic information

Entry
Database: PDB / ID: 6vtq
TitleCrystal structure of G16C human Galectin-7 mutant in complex with lactose
ComponentsGalectin-7
KeywordsSUGAR BINDING PROTEIN / Human Galectin-7 / lactose / G16C mutant / disulfide bond
Function / homology
Function and homology information


Differentiation of Keratinocytes in Interfollicular Epidermis in Mammalian Skin / heterophilic cell-cell adhesion / 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
alpha-lactose / Galectin-7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.95 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
Revision 1.4Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.5Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)30,9256
Polymers30,0562
Non-polymers8694
Water1,56787
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1910 Å2
ΔGint-3 kcal/mol
Surface area13370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)30.370, 66.210, 111.560
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: 15027.941 Da / Num. of mol.: 2 / Mutation: G16C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LGALS7, PIG1, LGALS7B / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P47929
#2: Polysaccharide beta-D-galactopyranose-(1-4)-alpha-D-glucopyranose / alpha-lactose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-lactose
DescriptorTypeProgram
DGalpb1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1a_1-5][a2112h-1b_1-5]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][b-D-Galp]{}}LINUCSPDB-CARE
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 87 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 1.87 Å3/Da / Density % sol: 34.15 %
Crystal growTemperature: 295.15 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.1 M Tris pH 8, 0.1 M Sodium Chloride, 25 % PEG3350, 7.5 mM alpha-lactose
Temp details: Room temperature

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Sep 28, 2019
RadiationMonochromator: ACCEL/BRUKER double crystal mocochromator (DCM,Si-111)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.95→42.66 Å / Num. obs: 17138 / % possible obs: 100 % / Redundancy: 12.59 % / CC1/2: 0.999 / Rmerge(I) obs: 0.107 / Rrim(I) all: 0.112 / Net I/σ(I): 16.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.95-2.0212.661.0373.117040.8681.081100
2.02-2.112.380.7684.216360.9410.802100
2.1-2.213.010.5586.317070.970.953100
2.2-2.3112.970.4028.416840.9850.41999.88
2.31-2.4612.410.30610.416700.9870.32100
2.46-2.6512.90.24413.217050.990.254100
2.65-2.9113.230.15918.517060.9960.166100
2.91-3.3312.750.09726.517330.9980.103100
3.33-4.212.020.06333.817330.9990.073100
4.2-42.6711.680.04839.618600.9990.0599.95

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation1.72 Å42.66 Å
Translation1.72 Å42.66 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: 1.95→42.66 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 25.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2445 1384 8.08 %
Rwork0.1847 15735 -
obs0.1898 17119 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 132.73 Å2 / Biso mean: 36.6079 Å2 / Biso min: 11.87 Å2
Refinement stepCycle: final / Resolution: 1.95→42.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2080 0 117 87 2284
Biso mean--39.07 35.59 -
Num. residues----264
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.95-2.020.33491370.298515651702100
2.02-2.10.3351320.22915041636100
2.1-2.20.26651390.191515681707100
2.2-2.310.24111350.183715421677100
2.31-2.460.26751350.185315381673100
2.46-2.650.26051380.192115661704100
2.65-2.910.26681380.190215671705100
2.91-3.330.24741400.183515951735100
3.33-4.20.21291400.159815901730100
4.2-42.660.22181500.17781700185099

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