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- PDB-4up6: Crystal structure of the wild-type diacylglycerol kinase refolded... -

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Basic information

Entry
Database: PDB / ID: 4up6
TitleCrystal structure of the wild-type diacylglycerol kinase refolded in the lipid cubic phase
ComponentsDIACYLGLYCEROL KINASE
KeywordsTRANSFERASE / 7.8 MAG / IN MESO / IN VITRO FOLDING / LIPID CUBIC PHASE / MEMBRANE PROTEIN / MONOACYLGLYCEROL / REFOLDING / RENATURATION
Function / homology
Function and homology information


diacylglycerol kinase (ATP) / lipid kinase activity / ATP-dependent diacylglycerol kinase activity / phosphatidic acid biosynthetic process / response to UV / ATP binding / metal ion binding / identical protein binding / membrane / 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: 3.801 Å
AuthorsLi, D. / Caffrey, M.
CitationJournal: Sci.Rep. / Year: 2014
Title: Renaturing Membrane Proteins in the Lipid Cubic Phase, a Nanoporous Membrane Mimetic.
Authors: Li, D. / Caffrey, M.
History
DepositionJun 13, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 22, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.2Apr 3, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.3Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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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)42,7583
Polymers42,7583
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7380 Å2
ΔGint-83.1 kcal/mol
Surface area16720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.390, 75.390, 197.200
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: 14252.625 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: K-12 / Plasmid: PTRCHISB-DGKA-WT / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): WH1061 / References: UniProt: P0ABN1, diacylglycerol kinase (ATP)
Sequence detailsAN N-TERMINAL TAG (GHHHHHHEL) WAS ADDED TO AID PROTEIN PURIFICATION. THE N-TERMINAL MET IS CLEAVED, ...AN N-TERMINAL TAG (GHHHHHHEL) WAS ADDED TO AID PROTEIN PURIFICATION. THE N-TERMINAL MET IS CLEAVED, AS SHOWN BY MASS-SPEC ANALYSIS.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.99 Å3/Da / Density % sol: 69.23 % / Description: NONE
Crystal growTemperature: 277 K / Method: lipidic cubic phase / pH: 5.6
Details: 3-5 %(V/V) 2-METHYL-2, 4-PENTANEDIOL, 0.1 M SODIUM CHLORIDE, 0.1 M LITHIUM NITRATE, 0.1 M SODIUM CITRATE/HCL PH 5.6. CRYSTALLIZED USING THE IN MESO (LIPIDIC CUBIC PHASE) METHOD AT 4 DEGREE ...Details: 3-5 %(V/V) 2-METHYL-2, 4-PENTANEDIOL, 0.1 M SODIUM CHLORIDE, 0.1 M LITHIUM NITRATE, 0.1 M SODIUM CITRATE/HCL PH 5.6. CRYSTALLIZED USING THE IN MESO (LIPIDIC CUBIC PHASE) METHOD AT 4 DEGREE CELSIUS WITH THE 7.8 MONOACYLGLYCEROL (7.8 MAG) AS THE HOSTING LIPID.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0332
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 16, 2012 / Details: K-B PAIR OF BIOMORPH MIRRORS
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 3.8→54.44 Å / Num. obs: 6532 / % possible obs: 95.5 % / Observed criterion σ(I): -3 / Redundancy: 6.4 % / Biso Wilson estimate: 136.72 Å2 / Rmerge(I) obs: 0.14 / Net I/σ(I): 9.2
Reflection shellResolution: 3.8→3.9 Å / Redundancy: 6.5 % / Rmerge(I) obs: 1.13 / Mean I/σ(I) obs: 1.7 / % possible all: 97.8

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3ZE4

3ze4


Resolution: 3.801→46.323 Å / SU ML: 0.59 / σ(F): 1.34 / Phase error: 43.17 / Stereochemistry target values: ML
Details: THERE ARE THREE IDENTICAL MONOMERS IN THE ASYMMETRIC UNIT. NCS RESTRAINTS WERE APPLIED FOR TORSION ANGLES DURING REFINEMENT.
RfactorNum. reflection% reflection
Rfree0.3715 318 4.9 %
Rwork0.3245 --
obs0.3263 6490 94.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 145.86 Å2
Refinement stepCycle: LAST / Resolution: 3.801→46.323 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2472 0 0 0 2472
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042513
X-RAY DIFFRACTIONf_angle_d0.8383425
X-RAY DIFFRACTIONf_dihedral_angle_d12.08854
X-RAY DIFFRACTIONf_chiral_restr0.045435
X-RAY DIFFRACTIONf_plane_restr0.003405
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.801-4.78810.36461660.33913075X-RAY DIFFRACTION97
4.7881-46.32620.37471520.31783097X-RAY DIFFRACTION93

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