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- PDB-4pcr: Crystal structure of Canavalia brasiliensis seed lectin (ConBr) c... -

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Basic information

Entry
Database: PDB / ID: 4pcr
TitleCrystal structure of Canavalia brasiliensis seed lectin (ConBr) complexed with Gamma-Aminobutyric Acid (GABA)
ComponentsConcanavalin-Br
KeywordsSUGAR BINDING PROTEIN
Function / homology
Function and homology information


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
GAMMA-AMINO-BUTANOIC ACID / ISOPROPYL ALCOHOL / : / DI(HYDROXYETHYL)ETHER / Concanavalin-Br
Similarity search - Component
Biological speciesCanavalia brasiliensis (Brazilian jackbean)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsDelatorre, P. / Rocha, B.A.M. / Silva-Filho, J.C. / Teixeira, C.S. / Cavada, B.S. / Nascimento, K.S. / Nbrega, R.B. / Nagano, C.S. / Sampaio, A.H. / Leal, R.B. / Neto, I.L.B.
CitationJournal: To Be Published
Title: Crystal structure of Canavalia brasiliensis seed lectin (ConBr) complexed with Gamma-Aminobutyric Acid (GABA)
Authors: Delatorre, P. / Rocha, B.A.M. / Silva-Filho, J.C. / Teixeira, C.S. / Cavada, B.S. / Nascimento, K.S. / Nbrega, R.B. / Nagano, C.S. / Sampaio, A.H. / Leal, R.B. / Neto, I.L.B.
History
DepositionApr 16, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 22, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 14, 2015Group: Data collection
Revision 1.2Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_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 2.0Nov 15, 2023Group: Atomic model / Data collection
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp_atom / chem_comp_bond
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _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
D: Concanavalin-Br
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,24716
Polymers51,1852
Non-polymers1,06214
Water1,72996
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4800 Å2
ΔGint-35 kcal/mol
Surface area18160 Å2
MethodPISA
2
A: Concanavalin-Br
D: Concanavalin-Br
hetero molecules

A: Concanavalin-Br
D: Concanavalin-Br
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,49432
Polymers102,3704
Non-polymers2,12428
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area13020 Å2
ΔGint-87 kcal/mol
Surface area32900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.410, 72.130, 68.390
Angle α, β, γ (deg.)90.00, 124.47, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 2 molecules AD

#1: Protein Concanavalin-Br / Con Br


Mass: 25592.428 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Canavalia brasiliensis (Brazilian jackbean)
References: UniProt: P55915

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Non-polymers , 7 types, 110 molecules

#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#4: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL / Isopropyl alcohol


Mass: 60.095 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#5: Chemical ChemComp-ABU / GAMMA-AMINO-BUTANOIC ACID / GAMMA(AMINO)-BUTYRIC ACID / Γ-Aminobutyric acid


Mass: 103.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H9NO2 / Comment: neurotransmitter, inhibitor*YM
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#7: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


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


Mass: 18.015 Da / Num. of mol.: 96 / 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: 2.4 Å3/Da / Density % sol: 48.79 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: TRIS 0.1 M pH 9.0, amonium sulfate 2.2 M

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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 165 mm / Detector: CCD / Date: Jun 10, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.43 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.579
11H+4/2L, -K, -L20.421
ReflectionResolution: 2.15→20.64 Å / Num. obs: 23808 / % possible obs: 89.25 % / Redundancy: 2.7 % / Net I/σ(I): 8
Reflection shellResolution: 2.15→2.27 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 2.5 / % possible all: 93.1

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Processing

Software
NameVersionClassification
SCALA5.8.0069data scaling
REFMAC5.8.0069refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3JU9

3ju9


Resolution: 2.15→20.64 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.941 / SU B: 11.911 / SU ML: 0.143 / Cross valid method: FREE R-VALUE / ESU R Free: 0.047 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23632 2431 10.3 %RANDOM
Rwork0.20023 ---
obs0.2041 21260 89.25 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.887 Å2
Baniso -1Baniso -2Baniso -3
1--8.06 Å20 Å2-15.91 Å2
2--6.63 Å20 Å2
3---1.43 Å2
Refinement stepCycle: 1 / Resolution: 2.15→20.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3548 0 62 96 3706
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0193676
X-RAY DIFFRACTIONr_bond_other_d0.0020.023447
X-RAY DIFFRACTIONr_angle_refined_deg1.9541.9534982
X-RAY DIFFRACTIONr_angle_other_deg1.33637942
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.3645462
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.83824.497149
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.77215570
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.8311514
X-RAY DIFFRACTIONr_chiral_restr0.1150.2568
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0214156
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02830
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_it2.672.7281863
X-RAY DIFFRACTIONr_mcbond_other2.6652.7281862
X-RAY DIFFRACTIONr_mcangle_it3.0294.0742318
X-RAY DIFFRACTIONr_mcangle_other3.0284.0742319
X-RAY DIFFRACTIONr_scbond_it3.2422.8671813
X-RAY DIFFRACTIONr_scbond_other3.2432.8671813
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.5724.2252665
X-RAY DIFFRACTIONr_long_range_B_refined3.3925.96215575
X-RAY DIFFRACTIONr_long_range_B_other3.39125.96215576
X-RAY DIFFRACTIONr_rigid_bond_restr5.27537123
X-RAY DIFFRACTIONr_sphericity_free10.785559
X-RAY DIFFRACTIONr_sphericity_bonded5.16157101
LS refinement shellResolution: 2.15→2.201 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.394 181 -
Rwork0.28 1497 -
obs--85.26 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.82860.18570.32981.38880.28680.72870.01390.03580.0684-0.1798-0.0469-0.3211-0.0382-0.03250.03290.1096-0.00070.06790.01890.04230.1929-2.8121-0.814222.3464
21.02630.21180.62951.64650.1351.0350.07430.115-0.0946-0.4025-0.0471-0.04980.0570.0756-0.02730.25170.0452-0.00230.02-0.01440.0265-20.4335-28.95229.948
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 237
2X-RAY DIFFRACTION2D1 - 237

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