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Basic information

Entry
Database: PDB / ID: 5d6i
TitleDgkA - CIM
ComponentsDiacylglycerol kinase
KeywordsTRANSFERASE / DIACYLGLYCEROL KINASE / CLLD / LIPID METABOLISM
Function / homology
Function and homology information


diacylglycerol kinase (ATP) / ATP-dependent diacylglycerol kinase activity / phosphatidic acid biosynthetic process / response to UV / phosphorylation / ATP binding / identical protein binding / membrane / metal ion binding / plasma membrane
Similarity search - Function
Helix Hairpins - #3610 / DAGK family / Diacylglycerol kinase, prokaryotic / Diacylglycerol kinase (DAGK) superfamily / Prokaryotic diacylglycerol kinase / Prokaryotic diacylglycerol kinase signature. / Helix Hairpins / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Diacylglycerol kinase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.091 Å
AuthorsMa, P. / Caffrey, M.
Funding support Ireland, Belgium, 2items
OrganizationGrant numberCountry
Science Foundation Ireland12/IA/1255 Ireland
Belgian National Funds for Scientific ResearchWELBIO CR-2012S-04 Belgium
CitationJournal: Nat Protoc / Year: 2017
Title: The cubicon method for concentrating membrane proteins in the cubic mesophase.
Authors: Ma, P. / Weichert, D. / Aleksandrov, L.A. / Jensen, T.J. / Riordan, J.R. / Liu, X. / Kobilka, B.K. / Caffrey, M.
History
DepositionAug 12, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Aug 17, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 30, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._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
Revision 1.2Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model
Item: _citation.country / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)42,7223
Polymers42,7223
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8160 Å2
ΔGint-92 kcal/mol
Surface area16150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.765, 72.765, 199.650
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

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


Mass: 14240.527 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: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.57 Å3/Da / Density % sol: 65.56 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase
Details: 6-11.5% MPD, 3% 1,4 butanediol, 0.1 M Li nitrate, 0.1 M NaCl, 0.1 M Na citrate pH 5.6.
PH range: 5.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.96861 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 28, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96861 Å / Relative weight: 1
ReflectionResolution: 3.09→45.76 Å / Num. obs: 11778 / % possible obs: 99.7 % / Redundancy: 7.9 % / Net I/σ(I): 1.4

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Processing

Software
NameVersionClassification
PHENIX1.9_1690refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ZE5

3ze5


Resolution: 3.091→45.758 Å / SU ML: 0.49 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 35.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.283 593 5.03 %
Rwork0.2662 --
obs0.267 11778 99.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.091→45.758 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2569 0 0 0 2569
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032615
X-RAY DIFFRACTIONf_angle_d0.4673565
X-RAY DIFFRACTIONf_dihedral_angle_d12.352886
X-RAY DIFFRACTIONf_chiral_restr0.018441
X-RAY DIFFRACTIONf_plane_restr0.002427
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.091-3.4020.39741470.32662711X-RAY DIFFRACTION99
3.402-3.8940.33441460.30322756X-RAY DIFFRACTION100
3.894-4.90520.26781490.25672798X-RAY DIFFRACTION100
4.9052-45.76250.26251510.25272920X-RAY DIFFRACTION99

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