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- PDB-4wv8: Crystal structure of a recombinant Vatairea macrocarpa seed lecti... -

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Basic information

Entry
Database: PDB / ID: 4wv8
TitleCrystal structure of a recombinant Vatairea macrocarpa seed lectin complexed with lactose
ComponentsSeed lectin
KeywordsSUGAR BINDING PROTEIN / Recombinant / Lectin / Legume / Dalbergieae
Function / homology
Function and homology information


carbohydrate binding / metal ion binding
Similarity search - Function
Legume lectin / Legume lectin, alpha chain, conserved site / Legume lectins alpha-chain signature. / Legume lectins beta-chain signature. / Legume lectin domain / Legume lectin, beta chain, Mn/Ca-binding site / Legume lectin domain / Jelly Rolls - #200 / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls ...Legume lectin / Legume lectin, alpha chain, conserved site / Legume lectins alpha-chain signature. / Legume lectins beta-chain signature. / Legume lectin domain / Legume lectin, beta chain, Mn/Ca-binding site / Legume lectin domain / Jelly Rolls - #200 / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
alpha-lactose / : / Seed lectin
Similarity search - Component
Biological speciesVatairea macrocarpa (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.83 Å
AuthorsSousa, B.L. / Silva-Filho, J.C. / Kumar, P. / Lyskowski, A. / Bezerra, G.A. / Delatorre, P. / Rocha, B.A.M. / Cunha, R.M.S. / Nagano, C.S. / Gruber, K. / Cavada, B.S.
CitationJournal: Int J Biochem Cell Biol / Year: 2016
Title: Structural characterization of a Vatairea macrocarpa lectin in complex with a tumor-associated antigen: A new tool for cancer research.
Authors: Bruno L Sousa / José C Silva-Filho / Prashant Kumar / Melissa A Graewert / Ronniery I Pereira / Rodrigo M S Cunha / Kyria S Nascimento / Gustavo A Bezerra / Plínio Delatorre / Kristina ...Authors: Bruno L Sousa / José C Silva-Filho / Prashant Kumar / Melissa A Graewert / Ronniery I Pereira / Rodrigo M S Cunha / Kyria S Nascimento / Gustavo A Bezerra / Plínio Delatorre / Kristina Djinovic-Carugo / Celso S Nagano / Karl Gruber / Benildo S Cavada /
Abstract: Legume lectins are the most thoroughly studied group of lectins and have been widely linked to many pathological processes. Their use as immunohistochemistry markers for cell profiling and cancer ...Legume lectins are the most thoroughly studied group of lectins and have been widely linked to many pathological processes. Their use as immunohistochemistry markers for cell profiling and cancer diagnosis have made these molecules important tools for immunological studies and have stimulated the prospection and characterization of new lectins. The crystal structures of a recombinant seed lectin from Vatairea macrocarpa (rVML) and its complexes with GalNAcα1-O-Ser, GalNAc and α-lactose, have been determined at 1.90, 1.97, 2.70 and 1.83Å resolution, respectively. Small angle X-ray scattering and calorimetry assays have confirmed the same pH stable oligomerization pattern and binding profiles proposed for its wild-type counterpart. In silico analyzes have explored the potential of this recombinant lectin as new tool for cancer research through a comparative profile with other legume lectins widely used for cancer diagnosis and prognosis. The results suggest the recognition of specific epitopes exhibited on different cancer cells as a process that relies on the disposition of hydrophobic clusters and charged regions around the lectin carbohydrate-binding site, favouring the anchorage of different groups in the antigen boundaries, highlighting the different potential of each analyzed lectin. In conclusion, the experimental results and comparative analysis show that rVML is as a promising tool for cancer research, able to bind with high affinity specific tumor-associated antigens, highly stable and easily produced.
History
DepositionNov 4, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jan 27, 2016Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.src_method / _entity.type / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_asym.entity_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Seed lectin
B: Seed lectin
C: Seed lectin
D: Seed lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,16216
Polymers105,4134
Non-polymers1,74912
Water12,448691
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9390 Å2
ΔGint-104 kcal/mol
Surface area35560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)152.644, 97.427, 78.667
Angle α, β, γ (deg.)90.000, 94.680, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Seed lectin / VML


Mass: 26353.154 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vatairea macrocarpa (plant) / Plasmid: pET-28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Codon-plus / References: UniProt: P81371
#2: Polysaccharide
beta-D-galactopyranose-(1-4)-alpha-D-glucopyranose / alpha-lactose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: 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: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#4: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 691 / Source method: isolated from a natural source / Formula: H2O

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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: 2.77 Å3/Da / Density % sol: 55.52 % / Description: Cubic crystal
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: Jeffamine 50% / PH range: 7.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.872 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 8, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.872 Å / Relative weight: 1
ReflectionResolution: 1.83→82.045 Å / Num. all: 100813 / Num. obs: 100813 / % possible obs: 99.4 % / Redundancy: 3.1 % / Rpim(I) all: 0.054 / Rrim(I) all: 0.097 / Rsym value: 0.081 / Net I/av σ(I): 6.368 / Net I/σ(I): 10.6 / Num. measured all: 314995
Reflection shell

Diffraction-ID: 1 / Redundancy: 3.1 % / Rejects: _

Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
1.83-1.930.2622.945343145940.1780.2624.198.6
1.93-2.040.1624.643740139100.1090.1626.399.8
2.04-2.180.122641305131290.0820.1228.199.9
2.18-2.360.0997.338373121950.0670.0999.899.8
2.36-2.580.097.935331112280.060.0910.899.5
2.58-2.890.075931807101380.050.07512.999.5
2.89-3.340.0659.52784889550.0430.06515.699.4
3.34-4.090.069.72327175550.040.0617.899.3
4.09-5.780.0598.91805858710.0390.05918.799.2
5.78-48.7140.0559.3991932380.0360.05518.698.5

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation4.47 Å48.71 Å
Translation4.47 Å48.71 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0071refinement
SCALA3.3.21data scaling
PHASER2.5.5phasing
PDB_EXTRACT3.15data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1FNY

1fny


Resolution: 1.83→82.045 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.936 / WRfactor Rfree: 0.1958 / WRfactor Rwork: 0.1584 / FOM work R set: 0.8835 / SU B: 2.288 / SU ML: 0.071 / SU R Cruickshank DPI: 0.1067 / SU Rfree: 0.107 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.107 / ESU R Free: 0.107 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1946 5032 5 %RANDOM
Rwork0.1567 95781 --
obs0.1586 95781 99.37 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 74.44 Å2 / Biso mean: 16.3 Å2 / Biso min: 6.78 Å2
Baniso -1Baniso -2Baniso -3
1-0.56 Å20 Å20.39 Å2
2---0.52 Å2-0 Å2
3----0.1 Å2
Refinement stepCycle: final / Resolution: 1.83→82.045 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7342 0 100 691 8133
Biso mean--19.77 24.38 -
Num. residues----950
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0197843
X-RAY DIFFRACTIONr_bond_other_d0.0010.027095
X-RAY DIFFRACTIONr_angle_refined_deg1.881.94610748
X-RAY DIFFRACTIONr_angle_other_deg0.891316463
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7845998
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.09225.015329
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.501151199
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.351520
X-RAY DIFFRACTIONr_chiral_restr0.1260.21238
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0218954
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021766
X-RAY DIFFRACTIONr_mcbond_it1.5421.4263932
X-RAY DIFFRACTIONr_mcbond_other1.541.4253931
X-RAY DIFFRACTIONr_mcangle_it2.3152.1254950
LS refinement shellResolution: 1.828→1.875 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.253 382 -
Rwork0.201 6938 -
all-7320 -
obs--97.37 %

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