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- PDB-8vcq: Crystal structure of the oligomeric rMcL-1 in complex with raffinose -

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Basic information

Entry
Database: PDB / ID: 8vcq
TitleCrystal structure of the oligomeric rMcL-1 in complex with raffinose
ComponentsGalactose-binding lectin
KeywordsSUGAR BINDING PROTEIN / Galactose binding lectin / rMcL-1
Function / homologygalactose binding / raffinose / ACETATE ION / alpha-D-galactopyranose / Galactose-binding lectin
Function and homology information
Biological speciesMytilus californianus (California mussel)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.09 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)152,33843
Polymers137,8068
Non-polymers14,53235
Water6,413356
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.520, 77.934, 156.285
Angle α, β, γ (deg.)90.000, 89.890, 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 , 1 types, 8 molecules ABCDEFGH

#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

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Sugars , 2 types, 28 molecules

#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.: 26
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
#3: 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.: 2 / 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

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Non-polymers , 6 types, 363 molecules

#4: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#5: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#6: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#7: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C2H3O2
#8: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 356 / 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: 2.81 Å3/Da / Density % sol: 56.18 %
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 20, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.09→49.34 Å / Num. obs: 159786 / % possible obs: 99.6 % / Redundancy: 7.8 % / Biso Wilson estimate: 36.97 Å2 / CC1/2: 0.804 / Rmerge(I) obs: 0.136 / Rpim(I) all: 0.048 / Rrim(I) all: 0.148 / Net I/σ(I): 29.2
Reflection shellResolution: 2.09→2.11 Å / Redundancy: 5.5 % / Mean I/σ(I) obs: 2.3 / Num. unique obs: 3759 / CC1/2: 0.704 / % possible all: 97.5

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Processing

Software
NameVersionClassification
PHENIX1.21rc1_5156refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.09→49.34 Å / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.0499
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2359 3796 2.38 %
Rwork0.2016 155990 -
obs0.2168 159786 89.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 39.46 Å2
Refinement stepCycle: LAST / Resolution: 2.09→49.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9599 0 942 356 10897
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004310865
X-RAY DIFFRACTIONf_angle_d1.032114786
X-RAY DIFFRACTIONf_chiral_restr0.05991754
X-RAY DIFFRACTIONf_plane_restr0.00611737
X-RAY DIFFRACTIONf_dihedral_angle_d14.17864314
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.09-2.120.35321010.31785075X-RAY DIFFRACTION56.5
2.12-2.160.35931580.32176743X-RAY DIFFRACTION75.16
2.16-2.20.35161660.3066783X-RAY DIFFRACTION77.14
2.2-2.250.33121640.29887097X-RAY DIFFRACTION79.08
2.25-2.30.29531660.29037288X-RAY DIFFRACTION81.16
2.3-2.350.30091590.27837332X-RAY DIFFRACTION82.66
2.35-2.410.29911640.27887458X-RAY DIFFRACTION84.11
2.41-2.470.29891650.27917646X-RAY DIFFRACTION85.83
2.47-2.550.30231780.27277821X-RAY DIFFRACTION87.11
2.55-2.630.31841840.25957939X-RAY DIFFRACTION88.96
2.63-2.720.29461900.25588080X-RAY DIFFRACTION90.7
2.72-2.830.23711900.24948230X-RAY DIFFRACTION92.46
2.83-2.960.30132010.22848403X-RAY DIFFRACTION93.91
2.96-3.120.23471940.22958469X-RAY DIFFRACTION94.74
3.12-3.310.28131970.22918578X-RAY DIFFRACTION96.06
3.31-3.570.20151970.20748603X-RAY DIFFRACTION96.74
3.57-3.930.21772030.18378665X-RAY DIFFRACTION97.18
3.93-4.490.23671950.16178701X-RAY DIFFRACTION97.41
4.49-5.660.19941910.16958615X-RAY DIFFRACTION96.6
5.66-49.340.19611970.20298700X-RAY DIFFRACTION97.58

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