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- PDB-4p14: Crystal structure of Canavalia brasiliensis (ConBr) complexed wit... -

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Basic information

Entry
Database: PDB / ID: 4p14
TitleCrystal structure of Canavalia brasiliensis (ConBr) complexed with adenine
ComponentsConcanavalin-Br
KeywordsSUGAR BINDING PROTEIN / Lectin / Canavalia brasiliensis / adenine
Function / homology
Function and homology information


D-mannose binding / toxin activity / 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
ADENINE / D-ALPHA-AMINOBUTYRIC ACID / : / Concanavalin-Br
Similarity search - Component
Biological speciesCanavalia brasiliensis (Brazilian jackbean)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsDelatorre, P. / Rocha, B.A.M. / Silva-Filho, J.C. / Teixeira, C.S. / Cavada, B.S. / Nascimento, K.S. / Neto, I.L.B. / Nobrega, R.B. / Nagano, C.S. / Sampaio, A.H. ...Delatorre, P. / Rocha, B.A.M. / Silva-Filho, J.C. / Teixeira, C.S. / Cavada, B.S. / Nascimento, K.S. / Neto, I.L.B. / Nobrega, R.B. / Nagano, C.S. / Sampaio, A.H. / Holanda, E. / Leal, R.B.
CitationJournal: To Be Published
Title: Crystal structure of Canavalia brasiliensis (ConBr) complexed with adenine
Authors: Delatorre, P. / Rocha, B.A.M. / Silva-Filho, J.C. / Teixeira, C.S. / Cavada, B.S. / Nascimento, K.S. / Neto, I.L.B. / Nobrega, R.B. / Nagano, C.S. / Sampaio, A.H. / Holanda, E. / Leal, R.B.
History
DepositionFeb 24, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 15, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Source and taxonomy
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity_src_nat / pdbx_initial_refinement_model / pdbx_struct_oper_list / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_nat.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation / _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
Revision 1.2Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Concanavalin-Br
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,2349
Polymers25,5921
Non-polymers6428
Water1,51384
1
A: Concanavalin-Br
hetero molecules

A: Concanavalin-Br
hetero molecules

A: Concanavalin-Br
hetero molecules

A: Concanavalin-Br
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,93636
Polymers102,3704
Non-polymers2,56632
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 area12630 Å2
ΔGint-100 kcal/mol
Surface area32130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.120, 70.940, 97.430
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-Br / Con Br


Mass: 25592.428 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Canavalia brasiliensis (Brazilian jackbean)
References: UniProt: P55915

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Non-polymers , 7 types, 92 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-ADE / ADENINE


Mass: 135.127 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H5N5
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-DBB / D-ALPHA-AMINOBUTYRIC ACID


Type: D-peptide linking / Mass: 103.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H9NO2
#7: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 84 / 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: 2.27 Å3/Da / Density % sol: 45.95 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 1.8 M ammonium sulfate, 0.2 M sodium chloride, 0.1 M HEPES, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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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: Jul 25, 2008
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1.43 Å / Relative weight: 1
ReflectionResolution: 2→22.56 Å / Num. obs: 15266 / % possible obs: 99 % / Redundancy: 9.5 % / Rmerge(I) obs: 0.067 / Net I/σ(I): 18.6
Reflection shellResolution: 2→2.05 Å / Redundancy: 9.4 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 4.8 / % possible all: 100

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Processing

SoftwareName: REFMAC / Version: 5.8.0049 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4H55

4h55


Resolution: 2→22.3 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.936 / SU B: 10.127 / SU ML: 0.125 / Cross valid method: THROUGHOUT / ESU R Free: 0.165 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22797 806 5 %RANDOM
Rwork0.17549 ---
obs0.17805 15266 99.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.118 Å2
Baniso -1Baniso -2Baniso -3
1-0.06 Å20 Å2-0 Å2
2---0.08 Å2-0 Å2
3---0.02 Å2
Refinement stepCycle: 1 / Resolution: 2→22.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1795 0 39 84 1918
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0191868
X-RAY DIFFRACTIONr_bond_other_d0.0030.021737
X-RAY DIFFRACTIONr_angle_refined_deg2.0011.9592534
X-RAY DIFFRACTIONr_angle_other_deg0.88734002
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.1255234
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.6524.60576
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.1815288
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.465157
X-RAY DIFFRACTIONr_chiral_restr0.1110.2289
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0212113
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02423
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_it3.953.342945
X-RAY DIFFRACTIONr_mcbond_other3.9473.34944
X-RAY DIFFRACTIONr_mcangle_it3.8925.0041176
X-RAY DIFFRACTIONr_mcangle_other3.8915.0051177
X-RAY DIFFRACTIONr_scbond_it4.2563.675922
X-RAY DIFFRACTIONr_scbond_other4.2433.675922
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.4355.3691359
X-RAY DIFFRACTIONr_long_range_B_refined4.26928.2822197
X-RAY DIFFRACTIONr_long_range_B_other4.25828.2442186
X-RAY DIFFRACTIONr_rigid_bond_restr5.77633601
X-RAY DIFFRACTIONr_sphericity_free18.132540
X-RAY DIFFRACTIONr_sphericity_bonded8.47653617
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3 68 -
Rwork0.227 1090 -
obs--100 %

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