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- PDB-3snm: Crystal structure of a lectin from Canavalia maritima seeds compl... -

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Basic information

Entry
Database: PDB / ID: 3snm
TitleCrystal structure of a lectin from Canavalia maritima seeds complexed with Indole-3-Acetic Acid
ComponentsConcanavalin-A
KeywordsMETAL BINDING PROTEIN / Sugar binding protein
Function / homology
Function and homology information


D-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
1H-INDOL-3-YLACETIC ACID / INDOLE / : / Concanavalin-A
Similarity search - Component
Biological speciesCanavalia lineata (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsDelatorre, P. / Silva-Filho, J.C. / Nobrega, R.B. / Rocha, B.C. / Cavada, B.S. / Gadelha, C.A.A. / Santi-Gadelha, T. / Alencar, K.L.
CitationJournal: Biochimie / Year: 2013
Title: Interactions between indole-3-acetic acid (IAA) with a lectin from Canavalia maritima seeds reveal a new function for lectins in plant physiology.
Authors: Delatorre, P. / Silva-Filho, J.C. / Rocha, B.A. / Santi-Gadelha, T. / da Nobrega, R.B. / Gadelha, C.A. / do Nascimento, K.S. / Nagano, C.S. / Sampaio, A.H. / Cavada, B.S.
History
DepositionJun 29, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 1, 2012Provider: repository / Type: Initial release
Revision 1.1Aug 21, 2013Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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_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_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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Concanavalin-A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,8825
Polymers25,4941
Non-polymers3874
Water1,08160
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Concanavalin-A
hetero molecules

A: Concanavalin-A
hetero molecules

A: Concanavalin-A
hetero molecules

A: Concanavalin-A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,52620
Polymers101,9774
Non-polymers1,54916
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-x,-y-1,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_545x,-y-1,-z1
Buried area9250 Å2
ΔGint-92 kcal/mol
Surface area32700 Å2
MethodPISA
3
A: Concanavalin-A
hetero molecules

A: Concanavalin-A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,76310
Polymers50,9882
Non-polymers7758
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_545x,-y-1,-z1
Buried area2850 Å2
ΔGint-47 kcal/mol
Surface area18130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.190, 70.740, 97.750
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Concanavalin-A / Con A


Mass: 25494.195 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Canavalia lineata (plant) / References: UniProt: P81460

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Non-polymers , 5 types, 64 molecules

#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-MN / MANGANESE (II) ION


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


Mass: 117.148 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H7N
#5: Chemical ChemComp-IAC / 1H-INDOL-3-YLACETIC ACID / INDOLE ACETIC ACID


Mass: 175.184 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H9NO2 / Comment: hormone*YM
#6: Water ChemComp-HOH / 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

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Sample preparation

CrystalDensity Matthews: 2.28 Å3/Da / Density % sol: 46.01 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: Buffer Tris 0.1 M pH 8.5, PEG 4000 30%, lithium sulphate 0.2M, VAPOR DIFFUSION, HANGING DROP, temperature 293K, temperature 293.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: D03B-MX1 / Wavelength: 1.433 Å
DetectorType: MAR CCD 130 mm / Detector: CCD / Date: May 10, 2009
RadiationMonochromator: YALE MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.433 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.941
11K, H, -L20.059
ReflectionResolution: 2.15→24.36 Å / Num. all: 12629 / Num. obs: 11903 / % possible obs: 96.4843 % / Observed criterion σ(I): 4

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Processing

Software
NameVersionClassification
iMOSFLMdata reduction
Cootmodel building
REFMAC5.5.0066refinement
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.15→24.36 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.907 / SU B: 8.562 / SU ML: 0.1 / Cross valid method: THROUGHOUT / ESU R Free: 0.042 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22539 584 4.7 %RANDOM
Rwork0.20627 ---
obs0.20714 11903 96.48 %-
all-12629 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.088 Å2
Baniso -1Baniso -2Baniso -3
1-1.07 Å20 Å20 Å2
2---0.34 Å20 Å2
3----0.73 Å2
Refinement stepCycle: LAST / Resolution: 2.15→24.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1755 0 24 60 1839
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.0221818
X-RAY DIFFRACTIONr_angle_refined_deg2.6541.9562476
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.9125229
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.84124.7374
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.90815279
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.852156
X-RAY DIFFRACTIONr_chiral_restr0.1720.2283
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0211378
X-RAY DIFFRACTIONr_mcbond_it1.7161.51150
X-RAY DIFFRACTIONr_mcangle_it2.65821861
X-RAY DIFFRACTIONr_scbond_it4.0283668
X-RAY DIFFRACTIONr_scangle_it5.4874.5615
X-RAY DIFFRACTIONr_rigid_bond_restr2.65431818
X-RAY DIFFRACTIONr_sphericity_free9.084366
X-RAY DIFFRACTIONr_sphericity_bonded4.43131777
LS refinement shellResolution: 2.154→2.21 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.229 47 -
Rwork0.209 812 -
obs--91.58 %

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