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- PDB-7cya: Saimiri boliviensis boliviensis galectin-13 with lactose -

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Basic information

Entry
Database: PDB / ID: 7cya
TitleSaimiri boliviensis boliviensis galectin-13 with lactose
ComponentsGalectin
KeywordsSUGAR BINDING PROTEIN / Saimiri boliviensis boliviensis galectin-13 with lactose
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
beta-lactose / Galectin
Similarity search - Component
Biological speciesSaimiri boliviensis boliviensis (Bolivian squirrel monkey)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.71 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

Downloads & links

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Assembly

Deposited unit
A: Galectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,8312
Polymers16,4891
Non-polymers3421
Water2,306128
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area590 Å2
ΔGint6 kcal/mol
Surface area7400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)33.529, 58.789, 40.833
Angle α, β, γ (deg.)90.000, 113.630, 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: Polysaccharide beta-D-galactopyranose-(1-4)-beta-D-glucopyranose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: beta-lactose
DescriptorTypeProgram
DGalpb1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5][a2112h-1b_1-5]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][b-D-Galp]{}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 128 / 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: 2.24 Å3/Da / Density % sol: 44.99 %
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: 1.71→19.6 Å / Num. obs: 15714 / % possible obs: 99.5 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.055 / Net I/σ(I): 10.4
Reflection shellResolution: 1.71→1.74 Å / Rmerge(I) obs: 0.545 / Num. unique obs: 835

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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: 1.71→19.03 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 21.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2095 1560 9.94 %
Rwork0.1739 14133 -
obs0.1774 15693 99.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 79.74 Å2 / Biso mean: 27.6958 Å2 / Biso min: 13.42 Å2
Refinement stepCycle: final / Resolution: 1.71→19.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1145 0 45 128 1318
Biso mean--28.89 34.91 -
Num. residues----139
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.71-1.770.28471410.239512861427100
1.77-1.830.28641390.221271141099
1.83-1.90.23851360.196212711407100
1.9-1.990.23351450.176912921437100
1.99-2.090.22421420.16961283142599
2.09-2.220.22221390.164212721411100
2.22-2.390.22121440.17031292143699
2.39-2.630.20191420.175312691411100
2.64-3.020.20211420.178712871429100
3.02-3.790.18161450.166413001445100
3.8-19.030.20111450.16521310145599

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