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- PDB-7n96: Crystal structure of D103A human Galectin-7 mutant -

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Basic information

Entry
Database: PDB / ID: 7n96
TitleCrystal structure of D103A human Galectin-7 mutant
ComponentsGalectin-7
KeywordsSUGAR BINDING PROTEIN / human galectin-7 / dimer interface mutant
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. / Jelly Rolls - #200 / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.38 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
Other governmentFonds de Recherche du Quebec - Sante (FRQ-S) - Research Scholar Senior Career Award (281993) Canada
Other governmentFonds de Recherche du Quebec - Sante (FRQ-S) - Junior 1 (251848) Canada
Natural Sciences and Engineering Research Council (NSERC, Canada)RGPIN-2017-06091 Canada
Other governmentFonds de Recherche du Quebec - Sante (FRQ-S) - Doctoral Training scholarship (287239) Canada
CitationJournal: Protein Sci. / Year: 2026
Title: Network-based allosteric analysis of galectin-7: Key residues dictate functional communication and stability.
Authors: Pham, N.T.H. / Pare, A. / Letourneau, M. / Fortier, M. / Chatenet, D. / St-Pierre, Y. / Lague, P. / Calmettes, C. / Doucet, N.
History
DepositionJun 16, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 25, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Mar 4, 2026Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _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)30,1205
Polymers29,8442
Non-polymers2763
Water1,15364
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.510, 67.110, 68.010
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: 14921.840 Da / Num. of mol.: 2 / Mutation: D103A
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: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 64 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 2.05 Å3/Da / Density % sol: 39.88 %
Crystal growTemperature: 295.15 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.1 M NaCl, 0.1 M Tris pH 8, 20 % PEG 6000 ,15% 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 19, 2019 / Details: 16 tiled fiber-optic tapers
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.38→47.77 Å / Num. obs: 10282 / % possible obs: 100 % / Redundancy: 9.6 % / CC1/2: 0.998 / Rmerge(I) obs: 0.154 / Rpim(I) all: 0.052 / Rrim(I) all: 0.163 / Net I/σ(I): 13.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.38-2.479.81.521.910030.7190.5021.60399.8
2.47-2.569.81.12.610080.8210.3651.161100
2.56-2.689.70.863.410140.890.2890.909100
2.68-2.829.80.753.710100.8890.2480.791100
2.82-39.70.4316.310090.9730.1440.455100
3-3.239.70.2849.110130.9780.0940.3100
3.23-3.559.50.15615.510330.9950.0530.165100
3.55-4.079.40.09722.910290.9970.0330.103100
4.07-5.139.50.05732.910520.9990.0190.06100
5.13-47.788.80.04635.811110.9990.0160.048100

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation1.96 Å47.77 Å
Translation1.96 Å47.77 Å

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Processing

Software
NameVersionClassification
PHENIX1.19.2-4158refinement
XDSdata reduction
XSCALEdata scaling
PHASER2.7.12phasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1bkz

1bkz


Resolution: 2.38→47.77 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 26.9 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2594 1031 10.04 %
Rwork0.2179 9235 -
obs0.2221 10266 99.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 130.97 Å2 / Biso mean: 52.5643 Å2 / Biso min: 23.4 Å2
Refinement stepCycle: final / Resolution: 2.38→47.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2089 0 42 64 2195
Biso mean--60.44 43.45 -
Num. residues----267
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052177
X-RAY DIFFRACTIONf_angle_d0.8822945
X-RAY DIFFRACTIONf_dihedral_angle_d14.761821
X-RAY DIFFRACTIONf_chiral_restr0.057308
X-RAY DIFFRACTIONf_plane_restr0.006400
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.38-2.510.31781470.274512771424
2.51-2.660.33741490.259212951444
2.66-2.870.38651440.282512991443
2.87-3.160.26611420.228413091451
3.16-3.610.24721470.208113131460
3.61-4.550.22191490.183213401489
4.55-47.770.23331530.212214021555

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