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- PDB-7dvm: DgkA structure in E.coli lipid bilayer -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 7dvm
TitleDgkA structure in E.coli lipid bilayer
ComponentsDiacylglycerol kinase
KeywordsMEMBRANE PROTEIN / Enzyme / Embedded in E.coli lipid bilayer / paramagnetic labelling / CS-Rosetta
Function / homology
Function and homology information


diacylglycerol kinase (ATP) / ATP-dependent diacylglycerol kinase activity / phosphatidic acid biosynthetic process / membrane => GO:0016020 / ATP binding / metal ion binding / plasma membrane
Similarity search - Function
DAGK family / Diacylglycerol kinase, prokaryotic / Diacylglycerol kinase (DAGK) superfamily / Prokaryotic diacylglycerol kinase / Prokaryotic diacylglycerol kinase signature.
Similarity search - Domain/homology
Diacylglycerol kinase
Similarity search - Component
Biological speciesEscherichia coli IAI39 (bacteria)
MethodSOLID-STATE NMR / distance geometry
AuthorsLi, J. / Yang, J.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)21605156 China
CitationJournal: Commun Biol / Year: 2021
Title: Structure of membrane diacylglycerol kinase in lipid bilayers.
Authors: Li, J. / Shen, Y. / Chen, Y. / Zhang, Z. / Ma, S. / Wan, Q. / Tong, Q. / Glaubitz, C. / Liu, M. / Yang, J.
History
DepositionJan 13, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 13, 2022Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Diacylglycerol kinase
B: Diacylglycerol kinase
C: Diacylglycerol kinase


Theoretical massNumber of molelcules
Total (without water)47,5803
Polymers47,5803
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: cross-linking
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area10370 Å2
ΔGint-94 kcal/mol
Surface area17000 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 20000structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Diacylglycerol kinase


Mass: 15860.163 Da / Num. of mol.: 3
Mutation: A14(R1A), Y16(R1A), A24(R1A), A29(R1A), C46(R1A), D51(R1A), V79(R1A), L116(R1A), I70L, C113A, V107D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli IAI39 (bacteria) / Strain: IAI39 / ExPEC / Gene: dgkA, ECIAI39_4463 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A0H3MWQ1, diacylglycerol kinase (ATP)
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: SOLID-STATE NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
113isotropic1NCA
123isotropic1DARR
133isotropic1NCACX
143isotropic1CONCA
153isotropic1NCOCX

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Sample preparation

DetailsType: liposome
Contents: 0.83 mg/uL 13C_15N no-cys-DgkA, 0.166 mg/uL 13C_15N A24C-DgkA, 0.166 mg/uL 13C_15N A29C-DgkA, 0.166 mg/uL 13C_15N 46C-DgkA, 0.166 mg/uL 13C_15N V79C-DgkA, proteoliposome
Label: 13C_15N_sample / Solvent system: proteoliposome
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.83 mg/uLno-cys-DgkA13C_15N3
0.166 mg/uLA24C-DgkA13C_15N3
0.166 mg/uLA29C-DgkA13C_15N3
0.166 mg/uL46C-DgkA13C_15N3
0.166 mg/uLV79C-DgkA13C_15N3
Sample conditionsIonic strength: 10 mM / Label: conditions_1 / pH: 6.6 / Pressure: 1 atm / Temperature: 272 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 800 MHz

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Processing

NMR software
NameDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
SparkyGoddardchemical shift assignment
CS-ROSETTAShen, Vernon, Baker and Baxstructure calculation
RefinementMethod: distance geometry / Software ordinal: 3
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 20000 / Conformers submitted total number: 10

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