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- PDB-4tzd: Crystal structure of Canavalia maritima lectin (ConM) complexed w... -

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Basic information

Entry
Database: PDB / ID: 4tzd
TitleCrystal structure of Canavalia maritima lectin (ConM) complexed with interleukin - 1 beta primer
Components
  • Concanavalin-A
  • DNA (5'-D(P*CP*G)-3')
  • DNA (5'-D(P*TP*C)-3')
KeywordsCarbohydrate binding protein/DNA / Carbohydrate binding protein / Carbohydrate binding protein-DNA complex
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 ...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
DNA / Concanavalin-A
Similarity search - Component
Biological speciesCanavalia lineata (plant)
Escherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.2 Å
AuthorsVieira, D.B.H.A. / Delatorre, P. / Rocha, B.A.M. / Teixeira, C.S. / Silva-Filho, J.C. / Lima, E.M. / Nobrega, R.B. / Cavada, B.S.
CitationJournal: To Be Published
Title: Crystal structure of Canavalia maritima lectin (ConM) complexed with interleukin 1 - beta primer
Authors: Vieira, D.B.H.A. / Delatorre, P. / Cavada, B.S. / Nobrega, R.B. / Teixeira, C.S. / Silva-Filho, J.C. / Lima, E.M. / Rocha, B.A.M.
History
DepositionJul 10, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 22, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 14, 2015Group: Data collection
Revision 1.2Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Concanavalin-A
D: Concanavalin-A
G: DNA (5'-D(P*CP*G)-3')
H: DNA (5'-D(P*TP*C)-3')


Theoretical massNumber of molelcules
Total (without water)52,7294
Polymers52,7294
Non-polymers00
Water1,820101
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)192.230, 192.230, 192.230
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number196
Space group name H-MF23

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Components

#1: Protein Concanavalin-A / Con A


Mass: 25494.195 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Canavalia lineata (plant) / References: UniProt: P81460
#2: DNA chain DNA (5'-D(P*CP*G)-3')


Mass: 573.430 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Interleukin 1 - beta primer / Source: (synth.) Escherichia coli (E. coli)
#3: DNA chain DNA (5'-D(P*TP*C)-3')


Mass: 1166.805 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Interleukin 1 - beta primer / Source: (synth.) Escherichia coli (E. coli)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 101 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.81 Å3/Da / Density % sol: 56.17 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.2 M Magnesium chloride hexahydrate, 0.1 M HEPES sodium 7.5, 30% v/v 2-Propanol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.459 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Aug 15, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.459 Å / Relative weight: 1
ReflectionResolution: 3.2→48.06 Å / Num. obs: 9248 / % possible obs: 94.7 % / Redundancy: 2.7 % / Net I/σ(I): 5.7

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Processing

SoftwareName: REFMAC / Version: 5.6.0117 / Classification: refinement
RefinementResolution: 3.2→39.24 Å / Cor.coef. Fo:Fc: 0.876 / Cor.coef. Fo:Fc free: 0.826 / SU B: 31.292 / SU ML: 0.546 / Cross valid method: FREE R-VALUE / ESU R Free: 0.651 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.31494 516 5.3 %RANDOM
Rwork0.24703 ---
obs0.25062 8755 99.12 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 56.968 Å2
Refinement stepCycle: 1 / Resolution: 3.2→39.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3518 80 0 101 3699
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0193682
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6571.9275027
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.095460
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.27224.797148
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.52715559
X-RAY DIFFRACTIONr_dihedral_angle_4_deg27.6071512
X-RAY DIFFRACTIONr_chiral_restr0.1110.2578
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212759
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.2→3.283 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.369 52 -
Rwork0.252 617 -
obs--98.67 %

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