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- PDB-5u3e: Crystal Structure of Native Lectin from Canavalia bonariensis See... -

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Basic information

Entry
Database: PDB / ID: 5u3e
TitleCrystal Structure of Native Lectin from Canavalia bonariensis Seeds (CaBo) complexed with alpha-methyl-D-mannoside
ComponentsCanavalia bonariensis seed lectin
KeywordsSUGAR BINDING PROTEIN / Canavalia bonariensis / lectin / alpha-methyl-D-mannoside.
Function / homology
Function and homology information


D-mannose binding / 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 ...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
methyl alpha-D-mannopyranoside / : / Lectin CaBo
Similarity search - Component
Biological speciesCanavalia bonariensis (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsSilva, M.T.L. / Osterne, V.J.S. / Pinto-Junior, V.R. / Santiago, M.Q. / Araripe, D.A. / Neco, A.H.B. / Silva-Filho, J.C. / Martins, J.L. / Rocha, C.R.C. / Leal, R.B. ...Silva, M.T.L. / Osterne, V.J.S. / Pinto-Junior, V.R. / Santiago, M.Q. / Araripe, D.A. / Neco, A.H.B. / Silva-Filho, J.C. / Martins, J.L. / Rocha, C.R.C. / Leal, R.B. / Nascimento, K.S. / Cavada, B.S.
CitationJournal: Int. J. Biol. Macromol. / Year: 2018
Title: Canavalia bonariensis lectin: Molecular bases of glycoconjugates interaction and antiglioma potential.
Authors: Cavada, B.S. / Silva, M.T.L. / Osterne, V.J.S. / Pinto-Junior, V.R. / Nascimento, A.P.M. / Wolin, I.A.V. / Heinrich, I.A. / Nobre, C.A.S. / Moreira, C.G. / Lossio, C.F. / Rocha, C.R.C. / ...Authors: Cavada, B.S. / Silva, M.T.L. / Osterne, V.J.S. / Pinto-Junior, V.R. / Nascimento, A.P.M. / Wolin, I.A.V. / Heinrich, I.A. / Nobre, C.A.S. / Moreira, C.G. / Lossio, C.F. / Rocha, C.R.C. / Martins, J.L. / Nascimento, K.S. / Leal, R.B.
History
DepositionDec 2, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 23, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 30, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Sep 27, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.3Dec 6, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.name
Revision 1.4Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_label_atom_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 1.5Oct 4, 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

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Assembly

Deposited unit
A: Canavalia bonariensis seed lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,8404
Polymers25,5511
Non-polymers2893
Water2,126118
1
A: Canavalia bonariensis seed lectin
hetero molecules

A: Canavalia bonariensis seed lectin
hetero molecules

A: Canavalia bonariensis seed lectin
hetero molecules

A: Canavalia bonariensis seed lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,36216
Polymers102,2054
Non-polymers1,15712
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_555x,-y,-z1
Buried area9960 Å2
ΔGint-95 kcal/mol
Surface area33800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.169, 70.030, 111.649
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-459-

HOH

21A-510-

HOH

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Components

#1: Protein Canavalia bonariensis seed lectin


Mass: 25551.199 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Canavalia bonariensis (plant) / References: UniProt: P58906*PLUS
#2: Sugar ChemComp-MMA / methyl alpha-D-mannopyranoside / O1-METHYL-MANNOSE / methyl alpha-D-mannoside / methyl D-mannoside / methyl mannoside


Type: D-saccharide / Mass: 194.182 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C7H14O6
IdentifierTypeProgram
DManp[1Me]aCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
1-methyl-a-D-mannopyranoseCOMMON NAMEGMML 1.0
o1-methyl-mannoseIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Chemical ChemComp-MN / MANGANESE (II) ION


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


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 118 / 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: 2.45 Å3/Da / Density % sol: 49.89 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.8
Details: 100 mM Sodium Acetate, pH 4.8 10% PEG 3000 400 mM Zync Acetate
PH range: 4.2-5.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.42 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Oct 26, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.42 Å / Relative weight: 1
ReflectionResolution: 2.3→36.093 Å / Num. obs: 11449 / % possible obs: 99.6 % / Redundancy: 5.9 % / Biso Wilson estimate: 22.93 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.108 / Rsym value: 0.108 / Net I/σ(I): 9.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Diffraction-ID% possible all
2.3-2.425.90.250.949199.1
7.27-47.315.50.0690.994199.4

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Processing

Software
NameVersionClassification
SCALA3.3.22data scaling
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.22data extraction
iMOSFLMdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2OVU

2ovu


Resolution: 2.3→36.093 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.39
RfactorNum. reflection% reflection
Rfree0.2829 602 5.3 %
Rwork0.228 --
obs0.231 11360 98.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 68.74 Å2 / Biso mean: 24.5989 Å2 / Biso min: 6.64 Å2
Refinement stepCycle: final / Resolution: 2.3→36.093 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1792 0 15 118 1925
Biso mean--26.75 29.1 -
Num. residues----235
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091844
X-RAY DIFFRACTIONf_angle_d1.0682514
X-RAY DIFFRACTIONf_chiral_restr0.067292
X-RAY DIFFRACTIONf_plane_restr0.006324
X-RAY DIFFRACTIONf_dihedral_angle_d14.876644
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3-2.53140.33681580.25122625278399
2.5314-2.89760.36821350.26162637277298
2.8976-3.65010.261460.21772692283898
3.6501-36.09710.25081630.21392804296799

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