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- PDB-8vcp: Crystal structure of dimeric rMcL-1 in complex with raffinose -

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Basic information

Entry
Database: PDB / ID: 8vcp
TitleCrystal structure of dimeric rMcL-1 in complex with raffinose
ComponentsGalactose-binding lectin
KeywordsSUGAR BINDING PROTEIN / Galactose binding lectin / rMcL-1
Function / homologygalactose binding / raffinose / ACETATE ION / Galactose-binding lectin
Function and homology information
Biological speciesMytilus californianus (California mussel)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.58 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)37,66911
Polymers34,4512
Non-polymers3,2189
Water4,756264
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.879, 40.948, 65.839
Angle α, β, γ (deg.)90.000, 106.500, 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

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Protein / Sugars , 2 types, 8 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-28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: UniProt: A0A0P0E482
#2: Polysaccharide
alpha-D-galactopyranose-(1-6)-alpha-D-glucopyranose-(1-2)-beta-D-fructofuranose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 504.438 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with reducing-end-to-reducing-end glycosidic bond
References: raffinose
DescriptorTypeProgram
DGalpa1-6DGlcpa1-2DFrufbGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,3,2/[ha122h-2b_2-5][a2122h-1a_1-5][a2112h-1a_1-5]/1-2-3/a2-b1_b6-c1WURCSPDB2Glycan 1.1.0
[][b-D-Fruf]{[(2+1)][a-D-Glcp]{[(6+1)][a-D-Galp]{}}}LINUCSPDB-CARE

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Non-polymers , 4 types, 267 molecules

#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Ca
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 264 / 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: 2.15 Å3/Da / Density % sol: 42.78 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.1 M HEPES, 50 mM sodium acetate, 23% PEG 4000

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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: Nov 17, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.58→36.46 Å / Num. obs: 39833 / % possible obs: 99.33 % / Redundancy: 8.4 % / Biso Wilson estimate: 15.32 Å2 / CC1/2: 0.9 / Rmerge(I) obs: 0.094 / Rpim(I) all: 0.029 / Rrim(I) all: 0.098 / Net I/σ(I): 53.7
Reflection shellResolution: 1.58→1.62 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 4.7 / Num. unique obs: 2462 / CC1/2: 0.868 / % possible all: 98.8

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Processing

Software
NameVersionClassification
PHENIX1.21rc1_5156refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.58→36.46 Å / SU ML: 0.1725 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.3965
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1849 1988 5 %
Rwork0.154 37791 -
obs0.1555 39779 99.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 18.46 Å2
Refinement stepCycle: LAST / Resolution: 1.58→36.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2411 0 182 264 2857
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0122757
X-RAY DIFFRACTIONf_angle_d1.42243760
X-RAY DIFFRACTIONf_chiral_restr0.0783439
X-RAY DIFFRACTIONf_plane_restr0.0125454
X-RAY DIFFRACTIONf_dihedral_angle_d15.18011110
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.58-1.620.30431320.21932462X-RAY DIFFRACTION91.43
1.62-1.660.21371450.192668X-RAY DIFFRACTION99.89
1.66-1.710.22691390.17072721X-RAY DIFFRACTION99.93
1.71-1.770.2391250.16472698X-RAY DIFFRACTION99.93
1.77-1.830.25021140.17552733X-RAY DIFFRACTION100
1.83-1.910.21141590.16162673X-RAY DIFFRACTION99.93
1.91-1.990.19131370.15482716X-RAY DIFFRACTION99.89
1.99-2.10.19421490.15022699X-RAY DIFFRACTION100
2.1-2.230.19631550.15432684X-RAY DIFFRACTION99.96
2.23-2.40.17861330.14512735X-RAY DIFFRACTION99.97
2.4-2.640.19641650.15542697X-RAY DIFFRACTION99.9
2.64-3.020.17451470.14912717X-RAY DIFFRACTION99.83
3.03-3.810.15581410.14382761X-RAY DIFFRACTION99.9
3.81-36.460.15391470.14682827X-RAY DIFFRACTION99.97

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