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- PDB-8vcm: Crystal structure of rMcL-1 in complex with galactose -

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Basic information

Entry
Database: PDB / ID: 8vcm
TitleCrystal structure of rMcL-1 in complex with galactose
ComponentsGalactose-binding lectin
KeywordsSUGAR BINDING PROTEIN / Galactose binding lectin / rMcL-1
Function / homologygalactose binding / alpha-D-galactopyranose / Galactose-binding lectin
Function and homology information
Biological speciesMytilus californianus (California mussel)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.21 Å
AuthorsHernandez-Santoyo, A. / Loera-Rubalcava, J.
Funding support Mexico, 1items
OrganizationGrant numberCountry
Not funded Mexico
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
Revision 1.1May 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 1.2May 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)35,5579
Polymers34,4512
Non-polymers1,1057
Water1,40578
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.217, 41.094, 67.938
Angle α, β, γ (deg.)90.000, 107.700, 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: Sugar
ChemComp-GLA / alpha-D-galactopyranose / alpha-D-galactose / D-galactose / galactose / ALPHA D-GALACTOSE


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C6H12O6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGalpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-galactopyranoseCOMMON NAMEGMML 1.0
a-D-GalpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GalSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 78 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.22 Å3/Da / Density % sol: 44.71 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2 M Na iodine, 0.1 M Bis-tris pronane pH 8.5, 20% PEG 3350

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Data collection

DiffractionMean temperature: 101 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Sep 27, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 27697 / % possible obs: 99.5 % / Redundancy: 5 % / Biso Wilson estimate: 36.45 Å2 / CC1/2: 0.861 / Rmerge(I) obs: 0.119 / Net I/σ(I): 27.2
Reflection shellResolution: 2.2→2.28 Å / Num. unique obs: 2235 / CC1/2: 0.861

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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: 2.21→34.69 Å / SU ML: 0.2661 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 26.9386
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2036 1387 5.01 %
Rwork0.1838 26310 -
obs0.1848 27697 93.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 40.62 Å2
Refinement stepCycle: LAST / Resolution: 2.21→34.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2387 0 73 78 2538
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00892535
X-RAY DIFFRACTIONf_angle_d1.15413434
X-RAY DIFFRACTIONf_chiral_restr0.0752380
X-RAY DIFFRACTIONf_plane_restr0.0209436
X-RAY DIFFRACTIONf_dihedral_angle_d14.7656902
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.21-2.290.33451220.25452235X-RAY DIFFRACTION78.88
2.29-2.380.3081380.24042671X-RAY DIFFRACTION95.45
2.38-2.490.3261410.26782682X-RAY DIFFRACTION95.31
2.49-2.620.33581360.24222664X-RAY DIFFRACTION95.11
2.62-2.780.28831430.25432636X-RAY DIFFRACTION94.62
2.78-30.27871370.22862627X-RAY DIFFRACTION93.1
3-3.30.24861350.20972677X-RAY DIFFRACTION95.39
3.3-3.770.17781460.1562769X-RAY DIFFRACTION97.46
3.78-4.750.12281410.1332679X-RAY DIFFRACTION95.53
4.76-34.690.16341480.15752670X-RAY DIFFRACTION94.98

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