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- PDB-8vcs: Crystal structure of the oligomeric rMcL-1 in complex with lactose -

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Basic information

Entry
Database: PDB / ID: 8vcs
TitleCrystal structure of the oligomeric rMcL-1 in complex with lactose
ComponentsGalactose-binding lectin
KeywordsSUGAR BINDING PROTEIN / Galactose binding lectin / Mytilus californianus / rMcL-1
Function / homologygalactose binding / alpha-lactose / beta-D-galactopyranose / Galactose-binding lectin
Function and homology information
Biological speciesMytilus californianus (California mussel)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.89 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

Downloads & links

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Assembly

Deposited unit
A: Galactose-binding lectin
B: Galactose-binding lectin
C: Galactose-binding lectin
D: Galactose-binding lectin
E: Galactose-binding lectin
F: Galactose-binding lectin
G: Galactose-binding lectin
H: Galactose-binding lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)143,77332
Polymers137,8068
Non-polymers5,96724
Water13,439746
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.908, 77.871, 155.796
Angle α, β, γ (deg.)90.000, 90.050, 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.: 8
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: Polysaccharide
beta-D-galactopyranose-(1-4)-alpha-D-glucopyranose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 11
Source method: isolated from a genetically manipulated source
Details: author indicated that there is missing GLC not build in model connecting to GAL., oligosaccharide
References: alpha-lactose
DescriptorTypeProgram
DGalpb1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1a_1-5][a2112h-1b_1-5]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][b-D-Galp]{}}LINUCSPDB-CARE
#3: Sugar
ChemComp-GAL / beta-D-galactopyranose / beta-D-galactose / D-galactose / galactose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C6H12O6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGalpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-galactopyranoseCOMMON NAMEGMML 1.0
b-D-GalpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GalSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 746 / 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: 2.81 Å3/Da / Density % sol: 56.28 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 18% PEG 4000, 50 mM sodium acetate, 0.1 M HEPES, 0.1 M lithium sulfate

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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: Jan 18, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.89→49.39 Å / Num. obs: 122227 / % possible obs: 97.1 % / Redundancy: 3.7 % / Biso Wilson estimate: 22.35 Å2 / CC1/2: 0.827 / Rmerge(I) obs: 0.048 / Rpim(I) all: 0.029 / Rrim(I) all: 0.062 / Net I/σ(I): 24.5
Reflection shellResolution: 1.89→1.92 Å / Redundancy: 2.4 % / Mean I/σ(I) obs: 2.6 / Num. unique obs: 5082 / CC1/2: 0.8 / % possible all: 90.4

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Processing

Software
NameVersionClassification
PHENIX1.21rc1_5156refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.89→49.39 Å / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.0758
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1883 6105 5.15 %
Rwork0.1673 112540 -
obs0.1687 118645 97.02 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.85 Å2
Refinement stepCycle: LAST / Resolution: 1.89→49.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9627 0 398 746 10771
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009510359
X-RAY DIFFRACTIONf_angle_d1.425214026
X-RAY DIFFRACTIONf_chiral_restr0.08551571
X-RAY DIFFRACTIONf_plane_restr0.01291749
X-RAY DIFFRACTIONf_dihedral_angle_d14.84083907
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.89-1.920.24642840.25655082X-RAY DIFFRACTION84.24
1.92-1.960.26072930.2225404X-RAY DIFFRACTION88.36
1.96-20.22642960.21535478X-RAY DIFFRACTION89.19
2-2.040.22342630.20555387X-RAY DIFFRACTION89.77
2.04-2.080.23032740.20455523X-RAY DIFFRACTION90.44
2.08-2.130.20953000.25529X-RAY DIFFRACTION90.57
2.13-2.180.22363030.1965566X-RAY DIFFRACTION91.17
2.18-2.240.22562990.19245539X-RAY DIFFRACTION91.46
2.24-2.310.19232690.18665656X-RAY DIFFRACTION92.83
2.31-2.380.19812690.18365704X-RAY DIFFRACTION93.42
2.38-2.470.20673090.19255689X-RAY DIFFRACTION93.09
2.47-2.570.20312820.18785695X-RAY DIFFRACTION93.67
2.57-2.680.20973390.18025713X-RAY DIFFRACTION93.18
2.68-2.820.20413170.18165674X-RAY DIFFRACTION93.49
2.82-30.18723090.16935788X-RAY DIFFRACTION94.05
3-3.230.19993100.17255794X-RAY DIFFRACTION94.66
3.23-3.560.18282720.16375872X-RAY DIFFRACTION95.46
3.56-4.070.15893270.13245759X-RAY DIFFRACTION94.13
4.07-5.130.12243030.10885887X-RAY DIFFRACTION95.04
5.13-49.390.18053150.15795973X-RAY DIFFRACTION94.88

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