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- PDB-7un2: Crystal structure of a lectin from Canavalia maritima seed (ConM)... -

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Basic information

Entry
Database: PDB / ID: 7un2
TitleCrystal structure of a lectin from Canavalia maritima seed (ConM) complexed with Indole-3-butyric acid
ComponentsConM
KeywordsSUGAR BINDING PROTEIN / Lectin / ConM / Auxin / Indole-3-butyric acid
Function / homology3-INDOLEBUTYRIC ACID / D-ALPHA-AMINOBUTYRIC ACID / :
Function and homology information
Biological speciesCanavalia rosea (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
Authorsde Sousa, J.P. / Bezerra, E.H.S. / Sales, M.V. / Queiroz, P.P. / da Silva, F.M.S. / Carvalho, C.P.S. / Freire, V.N. / Rocha, B.A.M.
Funding support Brazil, 1items
OrganizationGrant numberCountry
Brazilian National Council for Scientific and Technological Development (CNPq)313837/2020-1 Brazil
CitationJournal: To Be Published
Title: Structural analysis of Canavalia maritima lectin complexed with auxins
Authors: de Sousa, J.P. / Bezerra, E.H.S. / Sales, M.V. / Queiroz, P.P. / da Silva, F.M.S. / Carvalho, C.P.S. / Freire, V.N. / Rocha, B.A.M.
History
DepositionApr 8, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 19, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
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: ConM
B: ConM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,74012
Polymers50,9882
Non-polymers75110
Water6,287349
1
A: ConM
B: ConM
hetero molecules

A: ConM
B: ConM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,48024
Polymers101,9774
Non-polymers1,50320
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area10900 Å2
ΔGint-138 kcal/mol
Surface area32480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.990, 71.843, 98.868
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21221
Space group name HallP22ab(y,z,x)
Symmetry operation#1: x,y,z
#2: x+1/2,-y,-z+1/2
#3: -x,y,-z
#4: -x+1/2,-y,z+1/2

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein ConM


Mass: 25494.195 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Canavalia rosea (plant)

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Non-polymers , 7 types, 359 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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-3IB / 3-INDOLEBUTYRIC ACID


Mass: 203.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H13NO2 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#7: 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 / Feature type: SUBJECT OF INVESTIGATION
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 349 / 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: 2.37 Å3/Da / Density % sol: 48.05 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 100 mM HEPES pH 7.5, 4% PEG 400, 2.0 M ammonium sulfate

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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: Feb 28, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.458 Å / Relative weight: 1
ReflectionResolution: 1.8→33.99 Å / Num. obs: 45553 / % possible obs: 99.72 % / Redundancy: 2 % / Biso Wilson estimate: 20.09 Å2 / CC1/2: 1 / Net I/σ(I): 27.87
Reflection shellResolution: 1.8→1.864 Å / Redundancy: 2 % / Mean I/σ(I) obs: 4.58 / Num. unique obs: 4472 / CC1/2: 0.961 / % possible all: 99.78

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Processing

Software
NameVersionClassification
MxCuBEdata collection
autoPROCdata reduction
Aimlessdata scaling
PHASERphasing
PHENIX1.12refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2CY6

2cy6


Resolution: 1.8→33.99 Å / SU ML: 0.1977 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.3111
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2333 2221 4.88 %
Rwork0.203 43249 -
obs0.2045 45470 99.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 26.74 Å2
Refinement stepCycle: LAST / Resolution: 1.8→33.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3562 0 40 349 3951
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00893674
X-RAY DIFFRACTIONf_angle_d1.66545001
X-RAY DIFFRACTIONf_chiral_restr0.0703573
X-RAY DIFFRACTIONf_plane_restr0.0119642
X-RAY DIFFRACTIONf_dihedral_angle_d12.5361504
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.840.3191390.27212659X-RAY DIFFRACTION99.86
1.84-1.880.27121500.25692619X-RAY DIFFRACTION99.68
1.88-1.930.26531460.23792654X-RAY DIFFRACTION99.86
1.93-1.980.27741540.22142666X-RAY DIFFRACTION99.86
1.98-2.040.2571370.21062667X-RAY DIFFRACTION99.57
2.04-2.110.2421380.20182696X-RAY DIFFRACTION99.61
2.11-2.180.25561680.21332648X-RAY DIFFRACTION99.89
2.18-2.270.26061340.20982669X-RAY DIFFRACTION99.96
2.27-2.370.25891380.20532689X-RAY DIFFRACTION99.68
2.37-2.50.25071290.21112703X-RAY DIFFRACTION99.82
2.5-2.650.23271200.20982717X-RAY DIFFRACTION99.86
2.65-2.860.2651350.20692717X-RAY DIFFRACTION99.93
2.86-3.140.24351400.19962711X-RAY DIFFRACTION99.89
3.14-3.60.17821260.19292768X-RAY DIFFRACTION99.93
3.6-4.530.20471510.1772768X-RAY DIFFRACTION99.83
4.53-33.990.20381160.19622898X-RAY DIFFRACTION98.88

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