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- PDB-6l4m: Crystal structure of vicilin from Solanum lycopersicum (tomato) -

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Basic information

Entry
Database: PDB / ID: 6l4m
TitleCrystal structure of vicilin from Solanum lycopersicum (tomato)
ComponentsVicilin
KeywordsPLANT PROTEIN / Enzyme / superoxide dismutase activity / vicilin / 7S globulin
Function / homology
Function and homology information


Vicilin, N-terminal / Vicilin N terminal region / Cupin / Cupin 1 / Cupin / RmlC-like cupin domain superfamily / Jelly Rolls / RmlC-like jelly roll fold / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
2-HYDROXYBENZOIC ACID / Vicilin
Similarity search - Component
Biological speciesSolanum lycopersicum (tomato)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.302 Å
AuthorsJain, A. / Salunke, D.M.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2020
Title: Comparative study of 7S globulin from Corylus avellana and Solanum lycopersicum revealed importance of salicylic acid and Cu-binding loop in modulating their function.
Authors: Shikhi, M. / Jain, A. / Salunke, D.M.
History
DepositionOct 18, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 4, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 22, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.2Nov 22, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Vicilin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,6502
Polymers45,5121
Non-polymers1381
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: The crystal structure has one monomer per asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area350 Å2
ΔGint4 kcal/mol
Surface area17250 Å2
Unit cell
Length a, b, c (Å)135.980, 135.980, 135.980
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number197
Space group name H-MI23

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Components

#1: Protein Vicilin


Mass: 45511.875 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Solanum lycopersicum (tomato) / References: UniProt: B0JEU3
#2: Chemical ChemComp-SAL / 2-HYDROXYBENZOIC ACID / SALICYLIC ACID


Mass: 138.121 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H6O3
Has ligand of interestN

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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: 2.3 Å3/Da / Density % sol: 46.57 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 1.1 M Ammonium tartrate dibasic pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.976 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 4, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 3.3→40 Å / Num. obs: 6429 / % possible obs: 99.9 % / Redundancy: 4.8 % / Rmerge(I) obs: 0.105 / Net I/σ(I): 10.4
Reflection shellResolution: 3.3→3.36 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.401 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 640 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
iMOSFLMdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5CAD

5cad


Resolution: 3.302→39.254 Å / SU ML: 0.45 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.08
RfactorNum. reflection% reflection
Rfree0.2659 389 6.05 %
Rwork0.2075 --
obs0.2109 6426 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.302→39.254 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2836 0 10 0 2846
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032904
X-RAY DIFFRACTIONf_angle_d0.6253911
X-RAY DIFFRACTIONf_dihedral_angle_d16.2011738
X-RAY DIFFRACTIONf_chiral_restr0.045408
X-RAY DIFFRACTIONf_plane_restr0.004526
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3019-3.77930.33071230.24351988X-RAY DIFFRACTION100
3.7793-4.76030.241450.19811979X-RAY DIFFRACTION100
4.7603-39.25680.2611210.19822073X-RAY DIFFRACTION100

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