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- PDB-6kjx: Galectin-13 variant C138S -

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Basic information

Entry
Database: PDB / ID: 6kjx
TitleGalectin-13 variant C138S
ComponentsGalactoside-binding soluble lectin 13
KeywordsSUGAR BINDING PROTEIN / Galectin-13 variant C138S
Function / homology
Function and homology information


lysophospholipase activity / phospholipid metabolic process / nuclear matrix / carbohydrate binding / nuclear body / apoptotic process / nucleoplasm / 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
Galactoside-binding soluble lectin 13
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.53 Å
AuthorsSu, J.
CitationJournal: Glycobiology / Year: 2020
Title: Galectin-13/placental protein 13: redox-active disulfides as switches for regulating structure, function and cellular distribution.
Authors: Yang, T. / Yao, Y. / Wang, X. / Li, Y. / Si, Y. / Li, X. / Ayala, G.J. / Wang, Y. / Mayo, K.H. / Tai, G. / Zhou, Y. / Su, J.
History
DepositionJul 23, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 16, 2019Provider: repository / Type: Initial release
Revision 1.1Feb 19, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.2Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Galactoside-binding soluble lectin 13


Theoretical massNumber of molelcules
Total (without water)16,4021
Polymers16,4021
Non-polymers00
Water2,522140
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area6960 Å2
Unit cell
Length a, b, c (Å)53.617, 53.617, 113.810
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Galactoside-binding soluble lectin 13 / Galectin-13 / Gal-13 / Placental tissue protein 13 / Placental protein 13


Mass: 16401.734 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: variant C138S / Source: (gene. exp.) Homo sapiens (human) / Gene: LGALS13, PLAC8 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UHV8
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 140 / Source method: isolated from a natural source / Formula: H2O

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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: 2.49 Å3/Da / Density % sol: 50.67 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: Bis-Tris

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 21, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.53→19.52 Å / Num. obs: 25914 / % possible obs: 99.9 % / Redundancy: 9 % / Net I/σ(I): 25.2
Reflection shellResolution: 1.53→1.56 Å / Num. unique obs: 1255

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Processing

SoftwareName: PHENIX / Version: 1.12_2829 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.53→19.515 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 20.45
RfactorNum. reflection% reflection
Rfree0.2087 2000 7.74 %
Rwork0.1829 --
obs0.1849 25849 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 93.99 Å2 / Biso mean: 26.8174 Å2 / Biso min: 11.58 Å2
Refinement stepCycle: final / Resolution: 1.53→19.515 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1123 0 0 140 1263
Biso mean---35.7 -
Num. residues----139
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0111164
X-RAY DIFFRACTIONf_angle_d1.1591580
X-RAY DIFFRACTIONf_chiral_restr0.066173
X-RAY DIFFRACTIONf_plane_restr0.006203
X-RAY DIFFRACTIONf_dihedral_angle_d12.847690
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.53-1.56830.30051390.2628166799
1.5683-1.61070.28311400.24291661100
1.6107-1.6580.27231400.21411657100
1.658-1.71150.21471400.20581674100
1.7115-1.77270.25671410.20111688100
1.7727-1.84360.22251410.19331684100
1.8436-1.92740.19991400.19031672100
1.9274-2.02890.22541410.17861672100
2.0289-2.15590.20531420.18131700100
2.1559-2.32210.19841430.17681704100
2.3221-2.55530.18921450.1791723100
2.5553-2.92410.21471440.18381723100
2.9241-3.680.18111470.16761748100
3.68-19.5150.21051570.17931876100

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