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- PDB-8vcu: Crystal structure of the oligomeric rMcL-1 in complex with lactulose -

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Basic information

Entry
Database: PDB / ID: 8vcu
TitleCrystal structure of the oligomeric rMcL-1 in complex with lactulose
ComponentsGalactose-binding lectin
KeywordsSUGAR BINDING PROTEIN / Galactose binding lectin / rMcL-1
Function / homologygalactose binding / lactulose / ACETATE ION / NICKEL (II) ION / DI(HYDROXYETHYL)ETHER / Galactose-binding lectin
Function and homology information
Biological speciesMytilus californianus (California mussel)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.77 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,81426
Polymers68,9034
Non-polymers5,91122
Water11,367631
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.818, 64.626, 69.376
Angle α, β, γ (deg.)94.280, 103.900, 107.940
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

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Protein / Sugars , 2 types, 20 molecules ABCD

#1: Protein
Galactose-binding lectin / MCL


Mass: 17225.705 Da / Num. of mol.: 4
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)-beta-D-fructofuranose


Type: oligosaccharide, Oligosaccharide / Class: Water retention / Mass: 342.297 Da / Num. of mol.: 16
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: lactulose
DescriptorTypeProgram
DGalpb1-4DFrufb2-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[ha122h-2b_2-5][a2112h-1b_1-5]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
[][b-D-Fruf]{[(4+1)][b-D-Galp]{}}LINUCSPDB-CARE

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Non-polymers , 5 types, 637 molecules

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


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Ni
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 631 / 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: 2.36 Å3/Da / Density % sol: 47.92 %
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: Aug 17, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.77→50 Å / Num. obs: 111123 / % possible obs: 99.2 % / Redundancy: 5.2 % / Biso Wilson estimate: 11.76 Å2 / Rmerge(I) obs: 0.114 / Net I/σ(I): 19.8
Reflection shellResolution: 1.77→1.8 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.342 / Mean I/σ(I) obs: 3.4 / Num. unique obs: 3205 / CC1/2: 0.756 / % possible all: 97.1

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Processing

Software
NameVersionClassification
PHENIX1.21_5207refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.77→41.6 Å / SU ML: 0.216 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 22.4578
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2293 3325 2.99 %
Rwork0.1848 107798 -
obs0.1861 111123 90.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 13.86 Å2
Refinement stepCycle: LAST / Resolution: 1.77→41.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4777 0 394 631 5802
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00585342
X-RAY DIFFRACTIONf_angle_d1.30217266
X-RAY DIFFRACTIONf_chiral_restr0.0636840
X-RAY DIFFRACTIONf_plane_restr0.0074873
X-RAY DIFFRACTIONf_dihedral_angle_d13.11952045
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.77-1.80.34961010.24793205X-RAY DIFFRACTION64.72
1.8-1.820.27241340.23764003X-RAY DIFFRACTION80.3
1.82-1.850.32131270.23994013X-RAY DIFFRACTION81.21
1.85-1.880.25711140.23184055X-RAY DIFFRACTION81.97
1.88-1.920.30931240.21924075X-RAY DIFFRACTION82.89
1.92-1.950.26821030.21444217X-RAY DIFFRACTION84.24
1.95-1.990.241430.20464251X-RAY DIFFRACTION85.75
1.99-2.030.25771320.20924316X-RAY DIFFRACTION88.15
2.03-2.070.27191510.20464356X-RAY DIFFRACTION88.72
2.07-2.120.26031320.20584461X-RAY DIFFRACTION90.34
2.12-2.170.21051370.19514494X-RAY DIFFRACTION91.09
2.17-2.230.23181380.19444647X-RAY DIFFRACTION92.55
2.23-2.30.24371440.19434585X-RAY DIFFRACTION93.31
2.3-2.370.22481460.19094706X-RAY DIFFRACTION94.95
2.37-2.460.25191470.19974767X-RAY DIFFRACTION95.6
2.46-2.560.25071500.19884722X-RAY DIFFRACTION96.74
2.56-2.670.23861510.20154880X-RAY DIFFRACTION97.69
2.67-2.810.23921420.18914803X-RAY DIFFRACTION97.92
2.81-2.990.22491520.18484868X-RAY DIFFRACTION98.16
2.99-3.220.18231490.17644850X-RAY DIFFRACTION98.72
3.22-3.540.22911560.16794914X-RAY DIFFRACTION98.87
3.54-4.060.19381480.14834925X-RAY DIFFRACTION99.12
4.06-5.110.16881520.1334890X-RAY DIFFRACTION99.1
5.11-41.60.20261520.1724795X-RAY DIFFRACTION97.31

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