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- PDB-7cyb: Saimiri boliviensis boliviensis galectin-13 with glycerol -

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Basic information

Entry
Database: PDB / ID: 7cyb
TitleSaimiri boliviensis boliviensis galectin-13 with glycerol
ComponentsGalectin
KeywordsSUGAR BINDING PROTEIN / Saimiri boliviensis boliviensis galectin-13 with glycerol
Function / homology
Function and homology information


carbohydrate binding / apoptotic process
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 speciesSaimiri boliviensis boliviensis (Bolivian squirrel monkey)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsSu, J.
CitationJournal: Glycobiology / Year: 2021
Title: Actin binding to galectin-13/placental protein-13 occurs independently of the galectin canonical ligand-binding site.
Authors: Li, X. / Yao, Y. / Liu, T. / Gu, K. / Han, Q. / Zhang, W. / Ayala, G.J. / Liu, Y. / Na, H. / Yu, J. / Zhang, F. / Mayo, K.H. / Su, J.
History
DepositionSep 3, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 16, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 6, 2021Group: Database references / Category: citation / database_2
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 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

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Assembly

Deposited unit
A: Galectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,6733
Polymers16,4891
Non-polymers1842
Water3,027168
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area530 Å2
ΔGint-1 kcal/mol
Surface area7320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)33.407, 58.913, 40.701
Angle α, β, γ (deg.)90.000, 113.340, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Galectin / galectin-13


Mass: 16488.791 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saimiri boliviensis boliviensis (Bolivian squirrel monkey)
Production host: Escherichia coli (E. coli) / References: UniProt: A0A2K6TQH4
#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.: 168 / 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: 2.23 Å3/Da / Density % sol: 44.85 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: PEG

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 12, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.6→19.82 Å / Num. obs: 18965 / % possible obs: 98.9 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.034 / Net I/σ(I): 19.5
Reflection shellResolution: 1.6→1.63 Å / Rmerge(I) obs: 0.099 / Num. unique obs: 929

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6KJX

6kjx


Resolution: 1.6→19.82 Å / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 17.89 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1841 1900 10.03 %
Rwork0.1541 17043 -
obs0.1571 18943 98.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 69.84 Å2 / Biso mean: 19.3176 Å2 / Biso min: 6.47 Å2
Refinement stepCycle: final / Resolution: 1.6→19.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1145 0 28 168 1341
Biso mean--22.44 28.73 -
Num. residues----139
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 (%)
1.6-1.640.23611290.16881209133898
1.64-1.680.19571410.15851213135499
1.68-1.730.19931350.15681220135599
1.73-1.790.19691390.15521206134599
1.79-1.850.20121350.1541238137399
1.85-1.930.19831390.15291190132999
1.93-2.020.18391370.14951224136199
2.02-2.120.16691330.15651217135098
2.12-2.250.1881360.14511195133197
2.25-2.430.19391270.14621226135399
2.43-2.670.17891370.1541223136099
2.67-3.060.19711340.16141221135598
3.06-3.850.16471400.14881221136199
3.85-19.820.17691380.15891240137898

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