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- PDB-2l7c: Biophysical studies of lipid interacting regions of DGD2 in Arabi... -

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Basic information

Entry
Database: PDB / ID: 2l7c
TitleBiophysical studies of lipid interacting regions of DGD2 in Arabidopsis thaliana
ComponentsDigalactosyldiacylglycerol synthase 2, chloroplastic
KeywordsTRANSFERASE / amphipathic helix / glycosyltransferase / DGDG / diglycosyldiacylglycerol
Function / homology
Function and homology information


digalactosyldiacylglycerol synthase / galactolipid biosynthetic process / digalactosyldiacylglycerol synthase activity / chloroplast outer membrane / UDP-galactosyltransferase activity / glycolipid biosynthetic process / UDP-glycosyltransferase activity / cellular response to phosphate starvation
Similarity search - Function
Glycosyl transferase, family 1 / Glycosyl transferases group 1
Similarity search - Domain/homology
Digalactosyldiacylglycerol synthase 2, chloroplastic
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodSOLUTION NMR / torsion angle dynamics
Model detailsclosest to the average, model 10
AuthorsSzpryngiel, S. / Ge, C. / Iakovleva, I. / Lind, J. / Wieslander, A. / Maler, L.
CitationJournal: Biochemistry / Year: 2011
Title: Lipid interacting regions in phosphate stress glycosyltransferase atDGD2 from Arabidopsis thaliana.
Authors: Szpryngiel, S. / Ge, C. / Iakovleva, I. / Georgiev, A. / Lind, J. / Wieslander, A. / Maler, L.
History
DepositionDec 7, 2010Deposition site: BMRB / Processing site: RCSB
Revision 1.0Oct 19, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 25, 2012Group: Other
Revision 1.2Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.3May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Digalactosyldiacylglycerol synthase 2, chloroplastic


Theoretical massNumber of molelcules
Total (without water)2,2281
Polymers2,2281
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)23 / 100structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein/peptide Digalactosyldiacylglycerol synthase 2, chloroplastic


Mass: 2227.602 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: DGD2, At4g00550, F6N23.24
References: UniProt: Q8W1S1, digalactosyldiacylglycerol synthase

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-1H TOCSY
1212D 1H-1H NOESY

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Sample preparation

DetailsContents: 0.5 mM atDGD2_S227_245, 50 mM [U-2H] DPC, 10 % [U-2H] D2O, 50 mM sodium phosphate, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMatDGD2_S227_245-11
50 mMDPC-2[U-2H]1
10 %D2O-3[U-2H]1
50 mMsodium phosphate-41
Sample conditionsIonic strength: 50 / pH: 5.7 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 500 MHz

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Processing

NMR software
NameDeveloperClassification
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
SparkyGoddardchemical shift assignment
SparkyGoddarddata analysis
SparkyGoddardpeak picking
TopSpinBruker Biospincollection
TopSpinBruker Biospinprocessing
CYANAGuntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 23

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