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- PDB-2ef6: Canavalia gladiata lectin complexed with Man1-3Man-OMe -

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Basic information

Entry
Database: PDB / ID: 2ef6
TitleCanavalia gladiata lectin complexed with Man1-3Man-OMe
ComponentsConcanavalin A
KeywordsPLANT PROTEIN / Canavalia gladiata / lectin / seeds / dimannosides
Function / homology
Function and homology information


regulation of defense response to virus / monosaccharide binding / D-mannose binding / positive regulation of cell division / positive regulation of mitotic nuclear division / negative regulation of DNA-templated transcription / 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 ...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
Biological speciesCanavalia gladiata (sword bean)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsMoreno, F.B.M.B. / Bezerra, G.A. / Oliveira, T.M. / de Souza, E.P. / da Rocha, B.A.M. / Benevides, R.G. / Delatorre, P. / Cavada, B.S. / de Azevedo Jr., W.F.
CitationJournal: J.Struct.Biol. / Year: 2007
Title: Structural analysis of Canavalia maritima and Canavalia gladiata lectins complexed with different dimannosides: New insights into the understanding of the structure-biological activity ...Title: Structural analysis of Canavalia maritima and Canavalia gladiata lectins complexed with different dimannosides: New insights into the understanding of the structure-biological activity relationship in legume lectins
Authors: Bezerra, G.A. / Oliveira, T.M. / Moreno, F.B.M.B. / de Souza, E.P. / da Rocha, B.A.M. / Benevides, R.G. / Delatorre, P. / de Azevedo Jr., W.F. / Cavada, B.S.
History
DepositionFeb 21, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 30, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 11, 2017Group: Advisory / Database references / Source and taxonomy
Category: database_PDB_caveat / entity_src_nat ...database_PDB_caveat / entity_src_nat / struct_ref / struct_ref_seq
Item: _struct_ref_seq.ref_id
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_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_conn_angle / pdbx_validate_chiral / 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 / _database_PDB_caveat.text / _entity.pdbx_description / _entity.type / _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 / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_atom_id / _pdbx_validate_chiral.auth_comp_id / _pdbx_validate_chiral.auth_seq_id / _struct_asym.entity_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 25, 2023Group: 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: Concanavalin A
B: Concanavalin A
C: Concanavalin A
D: Concanavalin A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,05916
Polymers102,2534
Non-polymers1,80512
Water7,332407
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)69.391, 69.391, 161.298
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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Components

#1: Protein
Concanavalin A / lectin


Mass: 25563.322 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Canavalia gladiata (sword bean) / Tissue: seed / References: UniProt: P14894
#2: Polysaccharide
alpha-D-mannopyranose-(1-3)-methyl alpha-D-mannopyranoside


Type: oligosaccharide / Mass: 356.323 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManp[1Me]a1-OMEGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a1122h-1a_1-5_1*OC][a1122h-1a_1-5]/1-2/a3-b1WURCSPDB2Glycan 1.1.0
[][methyl]{[(1+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}}}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.: 407 / 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: 2.19 Å3/Da / Density % sol: 43.88 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: Sodium Formate, pH 4.5, 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: 1.43 Å
DetectorType: MAR CCD 130 mm / Detector: CCD / Date: Apr 1, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.43 Å / Relative weight: 1
ReflectionResolution: 2.07→40.29 Å / Num. obs: 48437 / Redundancy: 2.5 % / Rmerge(I) obs: 0.04 / Rsym value: 0.04 / Net I/σ(I): 10.7
Reflection shellHighest resolution: 2.07 Å / Rmerge(I) obs: 0.452 / Mean I/σ(I) obs: 2 / Rsym value: 0.452

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MARCCDdata collection
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1WUV

1wuv


Resolution: 2.1→33.92 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.915 / SU B: 5.188 / SU ML: 0.142 / Cross valid method: THROUGHOUT / ESU R: 0.272 / ESU R Free: 0.211 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24526 2524 5 %RANDOM
Rwork0.18935 ---
obs0.19224 47581 98.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.923 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.1→33.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7122 0 104 407 7633
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0227382
X-RAY DIFFRACTIONr_angle_refined_deg2.2671.95810064
X-RAY DIFFRACTIONr_dihedral_angle_1_deg14.3915928
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.56724.902306
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.363151134
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.3491524
X-RAY DIFFRACTIONr_chiral_restr0.1790.21176
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.025532
X-RAY DIFFRACTIONr_nbd_refined0.2390.24137
X-RAY DIFFRACTIONr_nbtor_refined0.320.25036
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.190.2621
X-RAY DIFFRACTIONr_metal_ion_refined0.1410.221
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2480.2127
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.210.229
X-RAY DIFFRACTIONr_mcbond_it1.1861.54712
X-RAY DIFFRACTIONr_mcangle_it1.95127520
X-RAY DIFFRACTIONr_scbond_it2.86932981
X-RAY DIFFRACTIONr_scangle_it4.14.52544
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.32 173 -
Rwork0.231 3467 -
obs--98.17 %

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