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- PDB-6a66: Placental protein 13/galectin-13 variant R53H with Tris -

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Basic information

Entry
Database: PDB / ID: 6a66
TitlePlacental protein 13/galectin-13 variant R53H with Tris
ComponentsGalactoside-binding soluble lectin 13
KeywordsSUGAR BINDING PROTEIN
Function / homology
Function and homology information


phosphatidylcholine 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: 1.4 Å
AuthorsSu, J.Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China31500637 China
CitationJournal: Biosci. Rep. / Year: 2018
Title: Resetting the ligand binding site of placental protein 13/galectin-13 recovers its ability to bind lactose
Authors: Su, J. / Cui, L. / Si, Y. / Song, C. / Li, Y. / Yang, T. / Wang, H. / Mayo, K.H. / Tai, G. / Zhou, Y.
History
DepositionJun 26, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 26, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,5212
Polymers16,3991
Non-polymers1221
Water1,946108
1
A: Galactoside-binding soluble lectin 13
hetero molecules

A: Galactoside-binding soluble lectin 13
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,0424
Polymers32,7982
Non-polymers2442
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Unit cell
Length a, b, c (Å)58.231, 92.060, 50.682
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number21
Space group name H-MC222
Components on special symmetry positions
IDModelComponents
11A-381-

HOH

21A-394-

HOH

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Components

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


Mass: 16398.750 Da / Num. of mol.: 1 / Fragment: UNP residues 2-139 / Mutation: R53H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LGALS13 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UHV8
#2: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 108 / Source method: isolated from a natural source / Formula: H2O
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: 2.12 Å3/Da / Density % sol: 42.11 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: PEG

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 1, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.4→19.115 Å / Num. obs: 27115 / % possible obs: 99.7 % / Redundancy: 6.2 % / Net I/σ(I): 12.1
Reflection shellResolution: 1.4→1.42 Å

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Processing

SoftwareName: PHENIX / Version: (1.10.1_2155: ???) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.4→19.115 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 29.43 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1949 2011 7.43 %
Rwork0.184 --
obs0.1848 27074 99.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 89.95 Å2 / Biso mean: 31.6709 Å2 / Biso min: 17.13 Å2
Refinement stepCycle: final / Resolution: 1.4→19.115 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1123 0 19 112 1254
Biso mean--38.81 38.81 -
Num. residues----138

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