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- PDB-8vck: Galactose-binding lectin from Mytilus californianus, Isoform 1 (r... -

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Basic information

Entry
Database: PDB / ID: 8vck
TitleGalactose-binding lectin from Mytilus californianus, Isoform 1 (rMcL-1)
ComponentsGalactose-binding lectin
KeywordsSUGAR BINDING PROTEIN / Glycan binding lectin
Function / homologygalactose binding / ACETATE ION / DI(HYDROXYETHYL)ETHER / Galactose-binding lectin
Function and homology information
Biological speciesMytilus californianus (California mussel)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.49 Å
AuthorsHernandez-Santoyo, A. / Loera-Rubalcava, J.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Int.J.Biol.Macromol. / Year: 2025
Title: A mytilectin from Mytilus californianus: Study of its unique galactoside interactions, oligomerization patterns, and antifungal activity.
Authors: Loera-Rubalcava, J. / Garcia-Maldonado, E. / Rodriguez-Romero, A. / Quintero-Martinez, A. / Macias-Rubalcava, M.L. / Cano-Sanchez, P. / Ramirez-Rodriguez, M.A. / Espinosa-Perez, G. / Hernandez-Santoyo, A.
History
DepositionDec 14, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 18, 2024Provider: repository / Type: Initial release
SupersessionJan 29, 2025ID: 6BFM
Revision 1.1Jan 29, 2025Group: Advisory / Category: pdbx_database_PDB_obs_spr
Revision 1.2May 7, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3May 21, 2025Group: Database references / Category: citation / Item: _citation.journal_volume

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Galactose-binding lectin
B: Galactose-binding lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,35312
Polymers34,4512
Non-polymers90210
Water6,287349
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3430 Å2
ΔGint-9 kcal/mol
Surface area12240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.960, 41.036, 66.224
Angle α, β, γ (deg.)90.000, 106.550, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Galactose-binding lectin


Mass: 17225.705 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mytilus californianus (California mussel)
Plasmid: pET-28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: UniProt: A0A0P0E482
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 349 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 2.18 Å3/Da / Density % sol: 43 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 18% POLYETHYLENE GLYCOL 4000, 50 mM SODIUM ACETATE, 0.1M HEPES, 0.1M LITHIUM SULFATE,

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Data collection

DiffractionMean temperature: 101 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5416 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Nov 16, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5416 Å / Relative weight: 1
ReflectionResolution: 1.49→36.56 Å / Num. obs: 48409 / % possible obs: 99 % / Redundancy: 9.9 % / Biso Wilson estimate: 15.03 Å2 / Rmerge(I) obs: 0.099 / Net I/σ(I): 52.7
Reflection shellResolution: 1.49→1.52 Å / Rmerge(I) obs: 0.099 / Num. unique obs: 2488

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Processing

Software
NameVersionClassification
PHENIX1.21rc1_5156refinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.49→36.56 Å / SU ML: 0.1514 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 19.1042
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1788 2426 5.05 %
Rwork0.1318 45587 -
obs0.1342 48013 99.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 18.69 Å2
Refinement stepCycle: LAST / Resolution: 1.49→36.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2401 0 59 349 2809
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01312603
X-RAY DIFFRACTIONf_angle_d1.40953517
X-RAY DIFFRACTIONf_chiral_restr0.1165367
X-RAY DIFFRACTIONf_plane_restr0.0121453
X-RAY DIFFRACTIONf_dihedral_angle_d13.1928985
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.49-1.520.30211350.21562488X-RAY DIFFRACTION91.97
1.52-1.550.2521460.17342667X-RAY DIFFRACTION99.58
1.55-1.590.23051380.14742702X-RAY DIFFRACTION99.72
1.59-1.630.21461420.13882678X-RAY DIFFRACTION99.54
1.63-1.670.22991480.13232664X-RAY DIFFRACTION99.68
1.67-1.720.19571330.13492674X-RAY DIFFRACTION99.61
1.72-1.780.21861330.13052694X-RAY DIFFRACTION99.65
1.78-1.840.18871400.13522703X-RAY DIFFRACTION99.48
1.84-1.910.18741420.12732638X-RAY DIFFRACTION99.11
1.91-20.1831480.12442684X-RAY DIFFRACTION99.26
2-2.110.18311480.12252685X-RAY DIFFRACTION99.61
2.11-2.240.16771340.12412688X-RAY DIFFRACTION99.33
2.24-2.410.1641440.1322701X-RAY DIFFRACTION99.58
2.41-2.650.18361470.14242682X-RAY DIFFRACTION98.95
2.65-3.040.19141580.14382681X-RAY DIFFRACTION98.85
3.04-3.820.1521520.12472729X-RAY DIFFRACTION99.79
3.82-36.560.14781380.12042829X-RAY DIFFRACTION99.83

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