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- PDB-3ax4: Three-dimensional structure of lectin from Dioclea violacea and c... -

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Basic information

Entry
Database: PDB / ID: 3ax4
TitleThree-dimensional structure of lectin from Dioclea violacea and comparative vasorelaxant effects with Dioclea rostrata
Componentslectin
KeywordsSUGAR BINDING PROTEIN / Jelly-roll / Lectin / Carbohydrate binding / Seed protein bodies
Function / homology
Function and homology information


mannose 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
: / Chem-XMM / Lectin
Similarity search - Component
Biological speciesDioclea violacea (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.613 Å
AuthorsBezerra, M.J.B. / Bezerra, G.A. / Martins, J.L. / Nascimento, K.S. / Nagano, C.S. / Gruber, K. / Assereuy, A.M. / Delatorre, P. / Rocha, B.A.M. / Cavada, B.S.
CitationJournal: Int.J.Biochem.Cell Biol. / Year: 2013
Title: Crystal structure of Dioclea violacea lectin and a comparative study of vasorelaxant properties with Dioclea rostrata lectin
Authors: Bezerra, M.J.B. / Rodrigues, N.V.F.C. / Pires, A.F. / Bezerra, G.A. / Nobre, C.B. / Alencar, K.L.L. / Soares, P.M.G. / Nascimento, K.S. / Nagano, C.S. / Martins, J.L. / Gruber, K. / Sampaio, ...Authors: Bezerra, M.J.B. / Rodrigues, N.V.F.C. / Pires, A.F. / Bezerra, G.A. / Nobre, C.B. / Alencar, K.L.L. / Soares, P.M.G. / Nascimento, K.S. / Nagano, C.S. / Martins, J.L. / Gruber, K. / Sampaio, A.H. / Delatorre, P. / Rocha, B.A.M. / Assreuy, A.M.S. / Cavada, B.S.
History
DepositionMar 29, 2011Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 4, 2012Provider: repository / Type: Initial release
Revision 1.1May 28, 2014Group: Database references
Revision 1.2Jul 29, 2020Group: Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _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.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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.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_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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
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: lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,0944
Polymers25,5901
Non-polymers5043
Water1,08160
1
A: lectin
hetero molecules

A: lectin
hetero molecules

A: lectin
hetero molecules

A: lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,37616
Polymers102,3614
Non-polymers2,01512
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_655-x+1,y,-z1
crystal symmetry operation4_565x,-y+1,-z1
Unit cell
Length a, b, c (Å)61.340, 66.110, 106.690
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-261-

HOH

21A-266-

HOH

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Components

#1: Protein lectin /


Mass: 25590.275 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Seeds / Source: (natural) Dioclea violacea (plant) / References: UniProt: I1SB09*PLUS
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Sugar ChemComp-XMM / 5-bromo-4-chloro-1H-indol-3-yl alpha-D-mannopyranoside / (2R,3S,4S,5S,6R)-2-(5-BROMO-4-CHLORO-1H-INDOL-3-YLOXY)-TETRAHYDRO-6-(HYDROXYMETHYL)-2H-PYRAN-3,4,5-TRIOL / (5-BROMO-4-CHLORO-3-INDOLYL)-Alpha-D-MANNOSE / 5-bromo-4-chloro-1H-indol-3-yl alpha-D-mannoside / 5-bromo-4-chloro-1H-indol-3-yl D-mannoside / 5-bromo-4-chloro-1H-indol-3-yl mannoside


Type: D-saccharide / Mass: 408.629 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C14H15BrClNO6
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 60 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.11 Å3/Da / Density % sol: 41.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.6
Details: 4.0M sodium formate, pH 7.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: D03B-MX1 / Wavelength: 1.47 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Aug 27, 2008
RadiationMonochromator: Silicon curly crystal with assimetric cut.Assimetry angle 7.25, condensed mode. Energy: 6 keV-12 keV (1 -2 ).
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.47 Å / Relative weight: 1
ReflectionResolution: 2.61→34.38 Å / Num. obs: 6354 / % possible obs: 92.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: 19.86 Å2

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASESphasing
PHENIX(phenix.refine: 1.7_650)refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.613→31.319 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8623 / SU ML: 0.33 / σ(F): 1.07 / Phase error: 21.54 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2737 299 4.71 %
Rwork0.228 --
obs0.2302 6353 92.5 %
Solvent computationShrinkage radii: 0.41 Å / VDW probe radii: 0.6 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 22.049 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso max: 64.89 Å2 / Biso mean: 23.8818 Å2 / Biso min: 8.61 Å2
Baniso -1Baniso -2Baniso -3
1-15.3558 Å2-0 Å2-0 Å2
2---8.4973 Å20 Å2
3----6.8585 Å2
Refinement stepCycle: LAST / Resolution: 2.613→31.319 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1776 0 25 60 1861
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0151851
X-RAY DIFFRACTIONf_angle_d0.852512
X-RAY DIFFRACTIONf_dihedral_angle_d13.64661
X-RAY DIFFRACTIONf_chiral_restr0.046284
X-RAY DIFFRACTIONf_plane_restr0.003319
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 2

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.6134-3.2920.30081540.2553297493
3.292-31.32150.25541450.211308092

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