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- PDB-2b7y: Fava Bean Lectin-Glucose Complex -

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Basic information

Entry
Database: PDB / ID: 2b7y
TitleFava Bean Lectin-Glucose Complex
Components
  • Favin alpha chain
  • Favin beta chain
KeywordsLECTIN / lectin-glucose complex / plant lectin / glycoprotein / carbohydrate binding protein / d-glucose / protein-carbohydrate complex
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-D-glucopyranose / : / Favin
Similarity search - Component
Biological speciesVicia faba (fava bean)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3 Å
AuthorsReeke Jr., G.N. / Becker, J.W.
Citation
Journal: Science / Year: 1986
Title: Three-dimensional structure of favin: saccharide binding-cyclic permutation in leguminous lectins
Authors: Reeke Jr., G.N. / Becker, J.W.
#1: Journal: J.Mol.Biol. / Year: 1974
Title: Favin, a crystalline lectin from Vicia faba
Authors: Wang, J.L. / Becker, J.W. / Edelman, G.M. / Reeke Jr., G.N.
#2: Journal: J.Biol.Chem. / Year: 1979
Title: The chemical characterization of favin, a lectin isolated from Vicia faba
Authors: Hemperly, J.J. / Hopp, T.P. / Becker, J.W. / Cunningham, B.A.
#3: Journal: J.Biol.Chem. / Year: 1982
Title: Amino acid sequence and variant forms of favin, a lectin from Vicia faba
Authors: Hopp, T.P. / Hemperly, J.J. / Cunningham, B.A.
History
DepositionOct 5, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 18, 2005Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / pdbx_validate_chiral / 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_atom_id / _atom_site.auth_comp_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _chem_comp.id / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Favin beta chain
B: Favin alpha chain
C: Favin beta chain
D: Favin alpha chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,08612
Polymers51,0934
Non-polymers9938
Water1448
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18710 Å2
ΔGint-115 kcal/mol
Surface area17860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.000, 89.300, 67.400
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsAsymmetric unit contains biological assembly, an alpha(2)-beta(2) tetramer

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Components

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Protein , 2 types, 4 molecules ACBD

#1: Protein Favin beta chain / lectin


Mass: 19973.172 Da / Num. of mol.: 2 / Fragment: residues 1-182 / Source method: isolated from a natural source / Details: extracted from seeds / Source: (natural) Vicia faba (fava bean) / References: UniProt: P02871
#2: Protein Favin alpha chain / lectin


Mass: 5573.199 Da / Num. of mol.: 2 / Fragment: residues 183-233 / Source method: isolated from a natural source / Details: extracted from seeds / Source: (natural) Vicia faba (fava bean) / References: UniProt: P02871

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Sugars , 2 types, 4 molecules

#3: Sugar ChemComp-GLC / alpha-D-glucopyranose / alpha-D-glucose / D-glucose / glucose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGlcpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-glucopyranoseCOMMON NAMEGMML 1.0
a-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 3 types, 12 molecules

#5: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#6: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.7 Å3/Da / Density % sol: 54.2 %
Description: The data were collected in 1974, the exact date is not available.
Crystal growTemperature: 277 K / Method: microdialysis / pH: 6.5
Details: 1 M glucose, 0.01 M sodium phosphate, pH 6.5, MICRODIALYSIS, temperature 277K

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: ELLIOTT GX-6 / Wavelength: 1.5418
DetectorType: FILM / Detector: FILM
RadiationMonochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3→46.18 Å / Num. all: 10599 / Num. obs: 10599 / % possible obs: 93 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 53.6 Å2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
REFMACrefinement
PDB_EXTRACT1.7data extraction
ROCKSdata scaling
CROWTHERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Pea lectin. Einspahr et al. (1986) J.Biol.Chem. 261:16518-16527.

Resolution: 3→46.18 Å / Cor.coef. Fo:Fc: 0.903 / Cor.coef. Fo:Fc free: 0.836 / SU B: 21.043 / SU ML: 0.387 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.563 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. EARLY REFINEMENT USED PROLSQ (AUTHORS: KONNERT AND HENDRICKSON) FOLLOWED BY TORSION-ANGLE MOLECULAR DYNAMICS REFINEMENT USING CNX (AUTHORS: ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. EARLY REFINEMENT USED PROLSQ (AUTHORS: KONNERT AND HENDRICKSON) FOLLOWED BY TORSION-ANGLE MOLECULAR DYNAMICS REFINEMENT USING CNX (AUTHORS: BRUNGER, ADAMS, CLORE, DELANO, GROS, GROSSE-KUNSTLEVE, JIANG, KUSZEWSKI, NILGES, PANNU, READ, RICE, SIMONSON, WARREN).
RfactorNum. reflection% reflectionSelection details
Rfree0.3 545 5.1 %RANDOM
Rwork0.224 ---
all0.227 10599 --
obs0.227 10599 92.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 25.733 Å2
Baniso -1Baniso -2Baniso -3
1-1.4 Å20 Å20 Å2
2---2.2 Å20 Å2
3---0.8 Å2
Refine analyzeLuzzati coordinate error obs: 0.346 Å
Refinement stepCycle: LAST / Resolution: 3→46.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3556 0 56 8 3620
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0223710
X-RAY DIFFRACTIONr_angle_refined_deg2.0561.9365072
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.8655452
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.08624.875160
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.96615546
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.472158
X-RAY DIFFRACTIONr_chiral_restr0.1170.2592
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022806
X-RAY DIFFRACTIONr_nbd_refined0.3030.22066
X-RAY DIFFRACTIONr_nbtor_refined0.3470.22622
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2330.2156
X-RAY DIFFRACTIONr_metal_ion_refined0.1880.25
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2910.214
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.320.21
X-RAY DIFFRACTIONr_mcbond_it0.951.52311
X-RAY DIFFRACTIONr_mcangle_it1.69223692
X-RAY DIFFRACTIONr_scbond_it1.84231613
X-RAY DIFFRACTIONr_scangle_it3.0574.51380
LS refinement shellResolution: 3→3.071 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.424 23 -
Rwork0.237 578 -
all-601 -
obs--73.2 %

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