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- PDB-5uzl: Brassica napus DGAT1 exosite -

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Basic information

Entry
Database: PDB / ID: 5uzl
TitleBrassica napus DGAT1 exosite
ComponentsO-acyltransferase
KeywordsTRANSFERASE / O-acyltransferase
Function / homology
Function and homology information


triglyceride biosynthetic process / diacylglycerol O-acyltransferase activity / O-acyltransferase activity / chloroplast envelope / membrane => GO:0016020 / endoplasmic reticulum membrane
Similarity search - Function
Diacylglycerol O-acyltransferase 1 / Sterol O-acyltransferase, ACAT/DAG/ARE types / Membrane bound O-acyl transferase, MBOAT / MBOAT, membrane-bound O-acyltransferase family
Similarity search - Domain/homology
O-acyltransferase / O-acyltransferase
Similarity search - Component
Biological speciesBrassica napus (rape)
MethodSOLUTION NMR / simulated annealing
AuthorsAcedo, J.Z. / Vederas, J.C.
CitationJournal: Plant Physiol. / Year: 2017
Title: Diacylglycerol Acyltransferase 1 Is Regulated by Its N-Terminal Domain in Response to Allosteric Effectors.
Authors: Caldo, K.M.P. / Acedo, J.Z. / Panigrahi, R. / Vederas, J.C. / Weselake, R.J. / Lemieux, M.J.
History
DepositionFeb 26, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 3, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: O-acyltransferase


Theoretical massNumber of molelcules
Total (without water)3,8771
Polymers3,8771
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide O-acyltransferase


Mass: 3877.332 Da / Num. of mol.: 1 / Fragment: UNP residues 81-113
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brassica napus (rape) / Gene: BnaCnng52810D, GSBRNA2T00056829001 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A078JH28, UniProt: K9LL63*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D NOESY
121isotropic12D TOCSY
131isotropic12D DQF-COSY
141isotropic12D 1H-15N HSQC

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Sample preparation

DetailsType: solution
Contents: 1 mM NA BnaDGAT1 exosite, 25 mM NA sodium chloride, 30 mM NA sodium phosphate, 0.01 % NA DSS, 90% H2O/10% D2O
Label: BnaDGAT1 / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMBnaDGAT1 exositeNA1
25 mMsodium chlorideNA1
30 mMsodium phosphateNA1
0.01 %DSSNA1
Sample conditionsIonic strength: 55 mM / Label: conditions_1 / pH: 6.3 / Pressure: 1 atm / Temperature: 300 K

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NMR measurement

NMR spectrometerType: Varian VNMRS / Manufacturer: Varian / Model: VNMRS / Field strength: 700 MHz

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Processing

NMR software
NameDeveloperClassification
CYANAGuntert, Mumenthaler and Wuthrichrefinement
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
NMRViewJohnson, One Moon Scientificchemical shift assignment
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRViewJohnson, One Moon Scientificpeak picking
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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