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- PDB-7n57: Crystal structure of R20A human Galectin-7 mutant in presence of ... -

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Basic information

Entry
Database: PDB / ID: 7n57
TitleCrystal structure of R20A human Galectin-7 mutant in presence of lactose
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 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. / Jelly Rolls - #200 / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
alpha-lactose / Galectin-7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.83 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)FRQ-S Research Scholar Senior Career Award (281993) Canada
Natural Sciences and Engineering Research Council (NSERC, Canada)RGPIN-2017-06091 Canada
Fonds de Recherche du Quebec - Sante (FRQS)FRQS Junior 1 (251848) Canada
Fonds de Recherche du Quebec - Sante (FRQS)FRQ-S Doctoral Training scholarship (287239) Canada
CitationJournal: To Be Published
Title: Crystal structure of R20A human Galectin-7 mutant
Authors: Pham, N.T.H. / Calmettes, C. / Doucet, N.
History
DepositionJun 4, 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

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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)30,7228
Polymers29,7592
Non-polymers9636
Water3,369187
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)30.220, 76.190, 111.190
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: 14879.734 Da / Num. of mol.: 2 / Mutation: R20A
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


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.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 187 / 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: 2.15 Å3/Da / Density % sol: 42.81 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 0.2M Sodium chloride, 0.1M Tris pH 8.0, 20% w/v PEG 6000
PH range: 8 / 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: 0.97952 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 9, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97952 Å / Relative weight: 1
ReflectionResolution: 1.46→44.91 Å / Num. obs: 45632 / % possible obs: 100 % / Redundancy: 7.064 % / Biso Wilson estimate: 18.57 Å2 / CC1/2: 0.986 / Rmerge(I) obs: 0.186 / Rrim(I) all: 0.202 / Χ2: 0.804 / Net I/σ(I): 5.12 / Num. measured all: 322349
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.46-1.57.2041.7551.0124031333633360.3461.89100
1.5-1.547.2271.5081.1623258321832180.461.625100
1.54-1.587.241.1841.4722893316231620.6061.274100
1.58-1.637.251.0111.7621998303530340.6961.088100
1.63-1.697.2530.8172.221823300930090.7590.88100
1.69-1.757.2750.6922.620857286728670.7980.745100
1.75-1.817.2580.5293.3620170277927790.8810.57100
1.81-1.887.220.3964.3319486270126990.9310.42699.9
1.88-1.977.1340.3115.3818285256425630.9540.336100
1.97-2.067.0860.2536.3417488246824680.9710.274100
2.06-2.187.0250.2267.0816692237723760.9690.244100
2.18-2.316.9720.27.8515541222922290.9740.216100
2.31-2.476.9510.188.2614624210621040.9660.19499.9
2.47-2.676.8930.1628.813407194619450.9820.17599.9
2.67-2.926.780.1519.4512415183118310.9850.164100
2.92-3.266.6870.13710.4411067165816550.9840.14999.8
3.26-3.776.6280.13211.039863149014880.9630.14499.9
3.77-4.626.6360.1311.48342125712570.9850.14100
4.62-6.536.4590.12111.236543101310130.9860.131100
6.53-44.915.9530.11910.835666015990.9850.13399.7

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation1.46 Å44.91 Å
Translation1.46 Å44.91 Å

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Processing

Software
NameVersionClassification
PHENIX1.19.2-4158refinement
XSCALEdata scaling
PHASER2.7.12phasing
PDB_EXTRACT3.27data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4gal

4gal


Resolution: 1.83→44.91 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 18.87 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2082 1175 5 %
Rwork0.1711 22318 -
obs0.173 23493 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 134.73 Å2 / Biso mean: 28.534 Å2 / Biso min: 5.88 Å2
Refinement stepCycle: final / Resolution: 1.83→44.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2084 0 133 189 2406
Biso mean--48.73 35.51 -
Num. residues----267
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112255
X-RAY DIFFRACTIONf_angle_d1.2063071
X-RAY DIFFRACTIONf_dihedral_angle_d14.067832
X-RAY DIFFRACTIONf_chiral_restr0.068339
X-RAY DIFFRACTIONf_plane_restr0.008410
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.83-1.910.24871450.190427522897
1.91-2.010.24071440.180127472891
2.01-2.140.21311440.179127232867
2.14-2.310.22041450.16527692914
2.31-2.540.1941460.172127592905
2.54-2.90.20051450.18327672912
2.91-3.660.20941480.162728152963
3.66-44.910.19641580.165729863144

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