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- PDB-7xac: Dimeric structure of human galectin-7 in complex with two glycerol -

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Basic information

Entry
Database: PDB / ID: 7xac
TitleDimeric structure of human galectin-7 in complex with two glycerol
ComponentsGalectin-7
KeywordsSUGAR BINDING PROTEIN / APOPTOSIS
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 / Resolution: 1.8 Å
AuthorsSi, Y.L.
Funding support China, 1items
OrganizationGrant numberCountry
Other government China
CitationJournal: Int J Mol Sci / Year: 2022
Title: Binding of Glycerol to Human Galectin-7 Expands Stability and Modulates Its Functions.
Authors: Liang, Y. / Wang, Y. / Zhu, X. / Cai, J. / Shi, A. / Huang, J. / Zhu, Q. / Si, Y.
History
DepositionMar 17, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 11, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 29, 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)30,3784
Polymers30,1942
Non-polymers1842
Water4,143230
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: isothermal titration calorimetry, Apoptosis inhibition assay
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.596, 64.984, 71.159
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: 15097.046 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LGALS7, PIG1, LGALS7B / Production host: Escherichia coli (E. coli) / References: UniProt: P47929
#2: 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
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 230 / 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: 2.05 Å3/Da / Density % sol: 40.06 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 20% PEG 3350, 0.2M Magnesium chloride, 0.1M Hepes pH7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.977 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 8, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.977 Å / Relative weight: 1
ReflectionResolution: 1.8→19.85 Å / Num. obs: 23618 / % possible obs: 99.7 % / Redundancy: 1 % / Rmerge(I) obs: 0.033 / Net I/σ(I): 18.6
Reflection shellResolution: 1.8→1.84 Å / Rmerge(I) obs: 0.001 / Num. unique obs: 1388

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1BKZ

1bkz


Resolution: 1.8→19.85 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 23.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2527 2000 8.49 %
Rwork0.2004 21570 -
obs0.2048 23570 99.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 66.57 Å2 / Biso mean: 18.9185 Å2 / Biso min: 1.6 Å2
Refinement stepCycle: final / Resolution: 1.8→19.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2116 0 12 230 2358
Biso mean--22.01 26.72 -
Num. residues----270
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8-1.840.28611400.22541512165299
1.85-1.890.25391400.219415151655100
1.89-1.950.24711390.22021496163598
1.95-2.010.28611410.221515151656100
2.01-2.090.24161420.207515321674100
2.09-2.170.26211410.207815261667100
2.17-2.270.28211400.20581499163999
2.27-2.390.27311420.211615441686100
2.39-2.540.27681420.21915371679100
2.54-2.730.3031440.225415411685100
2.73-3.010.25741440.214615551699100
3.01-3.440.24831450.18815611706100
3.44-4.320.21341460.16215771723100
4.33-19.850.21911540.187216601814100

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