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

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Basic information

Entry
Database: PDB / ID: 7uod
TitleCrystal structure of a lectin from Canavalia maritima seed (ConM) complexed with 2,4-dichloro-phenoxyacetic acid
ComponentsConM
KeywordsSUGAR BINDING PROTEIN / Lectin / Auxin / 2 / 4-Dichlorophenoxyacetic acid
Function / homology(2,4-DICHLOROPHENOXY)ACETIC ACID / D-ALPHA-AMINOBUTYRIC ACID / : / DI(HYDROXYETHYL)ETHER
Function and homology information
Biological speciesCanavalia rosea (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsSousa, 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: 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 12, 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

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Assembly

Deposited unit
A: ConM
B: ConM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,14417
Polymers50,9882
Non-polymers1,15615
Water5,693316
1
A: ConM
B: ConM
hetero molecules

A: ConM
B: ConM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,28834
Polymers101,9774
Non-polymers2,31130
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area11500 Å2
ΔGint-181 kcal/mol
Surface area33130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.182, 71.830, 98.809
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 , 8 types, 331 molecules

#2: Chemical ChemComp-DBB / D-ALPHA-AMINOBUTYRIC ACID


Type: D-peptide linking / Mass: 103.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H9NO2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#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-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#7: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#8: Chemical ChemComp-CFA / (2,4-DICHLOROPHENOXY)ACETIC ACID / 2,4-DICHLOROPHENOXYACETIC ACID


Mass: 221.037 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H6Cl2O3 / Feature type: SUBJECT OF INVESTIGATION
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 316 / 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: 48.07 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 100 mM HEPES, 2.0 M Ammonium sulfate, 4% PEG 400

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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: Mar 1, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.458 Å / Relative weight: 1
ReflectionResolution: 1.6→33.75 Å / Num. obs: 62417 / % possible obs: 93.31 % / Redundancy: 2 % / Biso Wilson estimate: 20.06 Å2 / CC1/2: 1 / Net I/σ(I): 26.14
Reflection shellResolution: 1.6→1.657 Å / Mean I/σ(I) obs: 3.44 / Num. unique obs: 5886 / CC1/2: 0.908 / % possible all: 92.26

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Processing

Software
NameVersionClassification
autoPROCdata reduction
Aimlessdata scaling
PHASERphasing
PDB-REDOrefinement
PHENIX1.18.2_3874refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2CY6

2cy6


Resolution: 1.6→33.75 Å / SU ML: 0.1818 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.1636
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2272 1983 3.18 %
Rwork0.199 60347 -
obs0.1998 62330 96.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24.91 Å2
Refinement stepCycle: LAST / Resolution: 1.6→33.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3543 0 61 316 3920
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0123668
X-RAY DIFFRACTIONf_angle_d1.29594984
X-RAY DIFFRACTIONf_chiral_restr0.083572
X-RAY DIFFRACTIONf_plane_restr0.0099638
X-RAY DIFFRACTIONf_dihedral_angle_d10.1579508
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.640.31071280.26174040X-RAY DIFFRACTION91.64
1.64-1.680.25671350.2484120X-RAY DIFFRACTION93.87
1.68-1.730.291360.23064192X-RAY DIFFRACTION94.25
1.73-1.790.2551450.21854211X-RAY DIFFRACTION95.13
1.79-1.850.2511430.21534210X-RAY DIFFRACTION95.17
1.85-1.930.25521330.20164232X-RAY DIFFRACTION95.91
1.93-2.020.22781450.20594277X-RAY DIFFRACTION96.11
2.02-2.120.22121410.1984306X-RAY DIFFRACTION96.88
2.12-2.250.25981420.19964352X-RAY DIFFRACTION97.17
2.26-2.430.26191410.19664349X-RAY DIFFRACTION97.65
2.43-2.670.20531420.19984414X-RAY DIFFRACTION98.06
2.67-3.060.21291490.19684448X-RAY DIFFRACTION98.82
3.06-3.850.21611460.18444517X-RAY DIFFRACTION99.07
3.85-33.750.20641570.19224679X-RAY DIFFRACTION98.57

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