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- PDB-2kdc: NMR Solution Structure of E. coli diacylglycerol kinase (DAGK) in... -

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Basic information

Entry
Database: PDB / ID: 2kdc
TitleNMR Solution Structure of E. coli diacylglycerol kinase (DAGK) in DPC micelles
ComponentsDiacylglycerol kinase
KeywordsTRANSFERASE / Membrane Protein / Kinase / DAGK / Cell inner membrane / Cell membrane / Membrane / Phospholipid biosynthesis / Transmembrane
Function / homology
Function and homology information


diacylglycerol kinase (ATP) / ATP-dependent diacylglycerol kinase activity / phosphatidic acid biosynthetic process / response to UV / ATP binding / identical protein binding / membrane / metal ion binding / plasma membrane
Similarity search - Function
Diacylglycerol kinase fold / Diacylglycerol kinase (DAGK) domain / DAGK family / Diacylglycerol kinase, prokaryotic / Diacylglycerol kinase (DAGK) superfamily / Prokaryotic diacylglycerol kinase / Prokaryotic diacylglycerol kinase signature. / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Diacylglycerol kinase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsVan Horn, W.D. / Kim, H. / Ellis, C.D. / Hadziselimovic, A. / Sulistijo, E.S. / Karra, M.D. / Tian, C. / Sonnichsen, F.D. / Sanders, C.R.
CitationJournal: Science / Year: 2009
Title: Solution nuclear magnetic resonance structure of membrane-integral diacylglycerol kinase
Authors: Van Horn, W.D. / Kim, H.J. / Ellis, C.D. / Hadziselimovic, A. / Sulistijo, E.S. / Karra, M.D. / Tian, C. / Sonnichsen, F.D. / Sanders, C.R.
History
DepositionJan 6, 2009Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jul 7, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Diacylglycerol kinase
B: Diacylglycerol kinase
C: Diacylglycerol kinase


Theoretical massNumber of molelcules
Total (without water)39,3733
Polymers39,3733
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)16 / 48structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Diacylglycerol kinase / DAGK / Diglyceride kinase / DGK


Mass: 13124.421 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: dgkA, b4042, JW4002 / Production host: Escherichia coli (E. coli) / References: UniProt: P0ABN1, diacylglycerol kinase (ATP)

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D TROSY 1H-15N HSQC
1243D TROSY HNCO
1343D TROSY HNCA
1443D TROSY HN(CO)CA
1543D TROSY CBCA(CO)NH
1643D TROSY HN(CA)CB
1753D 1H-15N TROSY - NOESY
1822D TROSY 1H-15N HQSC
1932D TROSY 1H-15N HQSC

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Sample preparation

Details
Solution-IDContentsSolvent system
11.5 mM [U-100% 15N] DAGK, 90% H2O/10% D2O90% H2O/10% D2O
21.4 mM [ U-15N; U-2H] DAGK, 90% H2O/10% D2O90% H2O/10% D2O
31.0 mM [U-100% 15N] DAGK, 90% H2O/10% D2O90% H2O/10% D2O
41.0 mM [U-13C; U-15N; U-2H] DAGK, 90% H2O/10% D2O90% H2O/10% D2O
51.0 mM [U-100% 13C; U-100% 15N; U-80% 2H] DAGK, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.5 mMDAGK-1[U-100% 15N]1
1.4 mMDAGK-2[ U-15N; U-2H]2
1.0 mMDAGK-3[U-100% 15N]3
1.0 mMDAGK-4[U-13C; U-15N; U-2H]4
1.0 mMDAGK-5[U-100% 13C; U-100% 15N; U-80% 2H]5
Sample conditionspH: 6.5 / Pressure: ambient / Temperature: 318 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE8001
Bruker AvanceBrukerAVANCE6002

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR NIH2.19Schwieters, Kuszewski, Tjandra and Clorestructure solution
X-PLOR NIH2.19Schwieters, Kuszewski, Tjandra and Clorerefinement
NMRView5Johnson, One Moon Scientificpeak picking
NMRView5Johnson, One Moon Scientificdata analysis
NMRView5Johnson, One Moon Scientificchemical shift assignment
TALOSCornilescu, Delaglio and Baxdihedral angle restraints
SparkyGoddarddata analysis
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxdata analysis
ProcheckNMRLaskowski and MacArthurdata analysis
RefinementMethod: simulated annealing / Software ordinal: 1 / Details: used refine.py from XPLOR-NIH
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 48 / Conformers submitted total number: 16

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