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- PDB-6vb8: Crystal structure of a lectin from Canavalia brasiliensis seed (C... -

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Basic information

Entry
Database: PDB / ID: 6vb8
TitleCrystal structure of a lectin from Canavalia brasiliensis seed (ConBr) complexed with indole-3-acetic acid
ComponentsConcanavalin-Br
KeywordsSUGAR BINDING PROTEIN / Canavalia brasiliensis / ConBr / IAA / indole-3-acetic acid / auxin / Lectin / ABU / alpha-aminobutyric acid
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 domain / Legume lectin, beta chain, Mn/Ca-binding site / : / Concanavalin A-like lectin/glucanase domain superfamily
Similarity search - Domain/homology
D-ALPHA-AMINOBUTYRIC ACID / 1H-INDOL-3-YLACETIC ACID / : / Concanavalin-Br
Similarity search - Component
Biological speciesCanavalia brasiliensis (Brazilian jackbean)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsBezerra, E.H.S. / Queiroz, P.P. / da Silva, F.M.S. / Girao, M.S. / Sales, M.V. / Paiva, C.P.S. / Freire, V.N. / Rocha, B.A.M.
Funding support Brazil, 1items
OrganizationGrant numberCountry
Coordination for the Improvement of Higher Education Personnel Brazil
CitationJournal: To Be Published
Title: Structural insights into phytohormone interaction to plant lectin ConBr
Authors: Bezerra, E.H.S. / Sales, M.V. / Girao, M.S. / da Silva, F.M.S. / Queiroz, P.P. / Paiva, C.P.S. / Freire, V.N. / Rocha, B.A.M.
History
DepositionDec 18, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 23, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
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)26,1298
Polymers25,5921
Non-polymers5367
Water79344
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)104,51532
Polymers102,3704
Non-polymers2,14528
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 area11970 Å2
ΔGint-166 kcal/mol
Surface area32120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.806, 72.427, 99.272
Angle α, β, γ (deg.)90.000, 90.000, 90.000
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, 51 molecules

#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#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-IAC / 1H-INDOL-3-YLACETIC ACID / INDOLE ACETIC ACID


Mass: 175.184 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H9NO2 / Feature type: SUBJECT OF INVESTIGATION
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 44 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.39 Å3/Da / Density % sol: 48.56 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 1.8 M ammonium sulfate, 0.2 M sodium chloride, 0.1 M HEPES, pH 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.458 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: May 18, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.458 Å / Relative weight: 1
ReflectionResolution: 2.2→49.69 Å / Num. obs: 12527 / % possible obs: 98.3 % / Redundancy: 11.9 % / CC1/2: 1 / Rmerge(I) obs: 0.046 / Rpim(I) all: 0.013 / Rrim(I) all: 0.048 / Net I/σ(I): 30.4
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 8.9 % / Rmerge(I) obs: 0.212 / Mean I/σ(I) obs: 8.9 / Num. unique obs: 1596 / CC1/2: 0.994 / Rpim(I) all: 0.073 / Rrim(I) all: 0.225 / % possible all: 88.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0241refinement
MOLREP10.2.31phasing
SCALA3.3.22data scaling
XDSMarch 15, 2019data reduction
MxCuBE2.3.0.1data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3JU9

3ju9


Resolution: 2.2→49.69 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.93 / SU B: 13.134 / SU ML: 0.159 / Cross valid method: FREE R-VALUE / σ(F): 0 / ESU R: 0.289 / ESU R Free: 0.21
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2356 660 5.3 %RANDOM
Rwork0.1985 ---
obs0.2005 11864 98.21 %-
Solvent computationIon probe radii: 1 Å / Shrinkage radii: 1 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 84.67 Å2 / Biso mean: 45.966 Å2 / Biso min: 28.47 Å2
Baniso -1Baniso -2Baniso -3
1--0.49 Å2-0 Å2-0 Å2
2--3.32 Å20 Å2
3----2.82 Å2
Refinement stepCycle: final / Resolution: 2.2→49.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1775 0 30 44 1849
Biso mean--62.07 44.24 -
Num. residues----233
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0131847
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171667
X-RAY DIFFRACTIONr_angle_refined_deg1.2741.6342513
X-RAY DIFFRACTIONr_angle_other_deg1.1691.5763877
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.5695233
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.42623.29382
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.66815286
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.655157
X-RAY DIFFRACTIONr_chiral_restr0.0440.2250
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022087
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02380
LS refinement shellResolution: 2.2→2.257 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.196 52 -
Rwork0.223 704 -
all-756 -
obs--81.2 %
Refinement TLS params.Method: refined / Origin x: 14.386 Å / Origin y: 14.256 Å / Origin z: 10.956 Å
111213212223313233
T0.0855 Å2-0.0789 Å2-0.0549 Å2-0.1445 Å20.0411 Å2--0.0483 Å2
L1.6721 °20.0019 °20.2804 °2-2.3176 °20.6925 °2--3.1791 °2
S-0.0536 Å °-0.135 Å °0.1084 Å °0.122 Å °-0.0557 Å °-0.2094 Å °-0.3376 Å °0.31 Å °0.1093 Å °

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