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- PDB-8vco: Crystal structure of rMcL-1 in complex with N-acetyl-D-galactosamine -

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Basic information

Entry
Database: PDB / ID: 8vco
TitleCrystal structure of rMcL-1 in complex with N-acetyl-D-galactosamine
ComponentsGalactose-binding lectin
KeywordsSUGAR BINDING PROTEIN / Galactose binding lectin / rMcL-1
Function / homologygalactose binding / : / 2-acetamido-2-deoxy-alpha-D-galactopyranose / ACETATE ION / DI(HYDROXYETHYL)ETHER / Galactose-binding lectin
Function and homology information
Biological speciesMytilus californianus (California mussel)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.66 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)36,58817
Polymers34,4512
Non-polymers2,13715
Water4,738263
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)73.951, 64.157, 75.694
Angle α, β, γ (deg.)90.000, 115.680, 90.000
Int Tables number5
Space group name H-MI121
Space group name HallC2y(x,y,-x+z)
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z+1/2
#4: -x+1/2,y+1/2,-z+1/2

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Components

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Protein / Sugars , 2 types, 7 molecules AB

#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-28 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: UniProt: A0A0P0E482
#2: Sugar
ChemComp-A2G / 2-acetamido-2-deoxy-alpha-D-galactopyranose / N-acetyl-alpha-D-galactosamine / 2-acetamido-2-deoxy-alpha-D-galactose / 2-acetamido-2-deoxy-D-galactose / 2-acetamido-2-deoxy-galactose / N-ACETYL-2-DEOXY-2-AMINO-GALACTOSE


Type: D-saccharide, alpha linking / Mass: 221.208 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGalpNAcaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-a-D-galactopyranosamineCOMMON NAMEGMML 1.0
a-D-GalpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GalNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 5 types, 273 molecules

#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-A1AAJ / N-Acetyl-D-Talosamine


Mass: 221.208 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-ACT / ACETATE ION


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


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


Mass: 18.015 Da / Num. of mol.: 263 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.37 Å3/Da / Density % sol: 48.01 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2 M potassium thiocyanate, 0.1 M Bis Tris propane, 20% w/v 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: May 11, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.66→46.22 Å / Num. obs: 37624 / % possible obs: 99.6 % / Redundancy: 7.3 % / Biso Wilson estimate: 12.28 Å2 / Rmerge(I) obs: 0.046 / Net I/σ(I): 23.3
Reflection shellResolution: 1.66→1.69 Å / Rmerge(I) obs: 0.564 / Num. unique obs: 1740

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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: 1.66→34.11 Å / SU ML: 0.1683 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.9805
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1818 1879 4.99 %
Rwork0.1507 35740 -
obs0.1523 37619 99.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 14.58 Å2
Refinement stepCycle: LAST / Resolution: 1.66→34.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2399 0 143 263 2805
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01522641
X-RAY DIFFRACTIONf_angle_d1.35843559
X-RAY DIFFRACTIONf_chiral_restr0.0982384
X-RAY DIFFRACTIONf_plane_restr0.0197448
X-RAY DIFFRACTIONf_dihedral_angle_d13.7094967
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.66-1.70.30041380.22672618X-RAY DIFFRACTION95.79
1.7-1.760.2431390.1892735X-RAY DIFFRACTION99.38
1.76-1.810.21021480.16332746X-RAY DIFFRACTION99.97
1.81-1.880.1961380.15212737X-RAY DIFFRACTION99.93
1.88-1.950.17061420.14732773X-RAY DIFFRACTION99.97
1.95-2.040.20131450.152753X-RAY DIFFRACTION100
2.04-2.150.18611480.1432739X-RAY DIFFRACTION99.93
2.15-2.280.2061450.14122730X-RAY DIFFRACTION100
2.28-2.460.191480.1452771X-RAY DIFFRACTION100
2.46-2.710.16671440.14642762X-RAY DIFFRACTION100
2.71-3.10.16251500.14182764X-RAY DIFFRACTION100
3.1-3.90.16351440.13882783X-RAY DIFFRACTION100
3.9-34.110.15861500.15442829X-RAY DIFFRACTION99.9

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