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- PDB-1n47: Isolectin B4 from Vicia villosa in complex with the Tn antigen -

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Basic information

Entry
Database: PDB / ID: 1n47
TitleIsolectin B4 from Vicia villosa in complex with the Tn antigen
ComponentsIsolectin B4
KeywordsSUGAR BINDING PROTEIN / cancer antigen / Vicia villosa lectin / glycoprotein Tn-binding protein / carbohydrate recognition
Function / homology
Function and homology information


carbohydrate binding / metal ion binding
Similarity search - Function
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
2-acetamido-2-deoxy-alpha-D-galactopyranose / : / SERINE / Lectin B4
Similarity search - Component
Biological speciesVicia villosa (hairy vetch)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsBabino, A. / Tello, D. / Rojas, A. / Bay, S. / Osinaga, E. / Alzari, P.M.
Citation
Journal: FEBS Lett. / Year: 2003
Title: The crystal structure of a plant lectin in complex with the Tn antigen
Authors: Babino, A. / Tello, D. / Rojas, A. / Bay, S. / Osinaga, E. / Alzari, P.M.
#1: Journal: FEBS Lett. / Year: 1997
Title: Amino acid sequence and three-dimensional structure of the Tn-specific isolectin B4 from Vicia villosa.
Authors: Osinaga, E. / Tello, D. / Batthyany, C. / Bianchet, M. / Tavares, G. / Duran, R. / Cervenansky, C. / Camoin, L. / Roseto, A. / Alzari, P.M.
History
DepositionOct 30, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 25, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 2, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
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 / 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_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / struct_asym / struct_conn / 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.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Apr 3, 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
Remark 999sequence The author maintains that the sequence for the exact isoform crystallized here has not yet ...sequence The author maintains that the sequence for the exact isoform crystallized here has not yet been deposited in any sequence database.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Isolectin B4
B: Isolectin B4
C: Isolectin B4
D: Isolectin B4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,80924
Polymers98,8414
Non-polymers3,96720
Water1,02757
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)85.510, 85.510, 153.650
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Isolectin B4


Mass: 24710.346 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Details: extracted from seeds / Source: (natural) Vicia villosa (hairy vetch) / Tissue: seed / References: UniProt: P56625

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Sugars , 2 types, 8 molecules

#2: Polysaccharide
alpha-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]2-acetamido-2-deoxy-beta- ...alpha-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 570.542 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpa1-3[DGlcpNAcb1-4]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-2-1/a3-b1_a4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(3+1)][a-L-Fucp]{}[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#6: Sugar
ChemComp-A2G / 2-acetamido-2-deoxy-alpha-D-galactopyranose / N-acetyl-alpha-D-galactosamine / 2-acetamido-2-deoxy-alpha-D-galactose / 2-acetamido-2-deoxy-D-galactose / 2-acetamido-2-deoxy-galactose / N-ACETYL-2-DEOXY-2-AMINO-GALACTOSE / N-Acetylgalactosamine


Type: D-saccharide, alpha linking / Mass: 221.208 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGalpNAcaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-a-D-galactopyranosamineCOMMON NAMEGMML 1.0
a-D-GalpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GalNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 4 types, 69 molecules

#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: Chemical
ChemComp-SER / SERINE / Serine


Type: L-peptide linking / Mass: 105.093 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H7NO3
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 57 / 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: 2.84 Å3/Da / Density % sol: 56.69 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.7
Details: acetate, MPD , pH 4.7, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
1170 mMacetate1reservoirpH4.7
218 %MPD1reservoir

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: SYNCHROTRON / Site: LURE / Beamline: DW32 / Wavelength: 0.93 Å
DetectorType: MARRESEARCH / Detector: AREA DETECTOR
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.93 Å / Relative weight: 1
ReflectionResolution: 2.7→20 Å / Num. obs: 30037 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.7 % / Rsym value: 0.107
Reflection shellResolution: 2.7→2.8 Å / Rsym value: 0.46 / % possible all: 99.8
Reflection
*PLUS
Num. measured all: 144637 / Rmerge(I) obs: 0.107
Reflection shell
*PLUS
Lowest resolution: 2.78 Å / % possible obs: 99.8 % / Rmerge(I) obs: 0.467

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMAC5refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: structure of unliganded lectin (from reference 1)

Resolution: 2.7→20 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.91 / SU B: 12.227 / SU ML: 0.251 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.329
RfactorNum. reflection% reflectionSelection details
Rfree0.23766 1505 5 %RANDOM
Rwork0.18787 ---
obs0.19034 28662 99.9 %-
all-28662 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 33.566 Å2
Baniso -1Baniso -2Baniso -3
1-0.34 Å20 Å20 Å2
2--0.34 Å20 Å2
3----0.68 Å2
Refinement stepCycle: LAST / Resolution: 2.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6992 0 244 57 7293
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0217412
X-RAY DIFFRACTIONr_angle_refined_deg1.6961.96210180
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.4853928
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.311151072
X-RAY DIFFRACTIONr_chiral_restr0.1030.21236
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025640
X-RAY DIFFRACTIONr_nbd_refined0.2530.32999
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1360.5642
X-RAY DIFFRACTIONr_metal_ion_refined0.0850.58
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1910.37
X-RAY DIFFRACTIONr_mcbond_it0.6441.54676
X-RAY DIFFRACTIONr_mcangle_it1.22727520
X-RAY DIFFRACTIONr_scbond_it1.68932736
X-RAY DIFFRACTIONr_scangle_it2.7864.52660
LS refinement shellResolution: 2.7→2.769 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.419 104
Rwork0.241 2084
Refinement
*PLUS
Highest resolution: 2.7 Å / Lowest resolution: 20 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.238 / Rfactor Rwork: 0.188
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.014
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.7

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