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- PDB-5d57: In meso X-ray crystallography structure of diacylglycerol kinase,... -

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Basic information

Entry
Database: PDB / ID: 5d57
TitleIn meso X-ray crystallography structure of diacylglycerol kinase, DgkA, at 100 K
ComponentsDiacylglycerol kinase
KeywordsTRANSFERASE
Function / homology
Function and homology information


diacylglycerol kinase (ATP) / ATP-dependent diacylglycerol kinase activity / phosphatidic acid biosynthetic process / response to UV / phosphorylation / ATP binding / membrane / identical protein binding / 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
(2S)-2,3-DIHYDROXYPROPYL(7Z)-PENTADEC-7-ENOATE / Diacylglycerol kinase
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsHuang, C.-Y. / Howe, N. / Olieric, V. / Wang, M. / Caffrey, M.
Funding support Ireland, 1items
OrganizationGrant numberCountry
Science Foundation Ireland12/IA/1255 Ireland
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2016
Title: In meso in situ serial X-ray crystallography of soluble and membrane proteins at cryogenic temperatures.
Authors: Huang, C.Y. / Olieric, V. / Ma, P. / Howe, N. / Vogeley, L. / Liu, X. / Warshamanage, R. / Weinert, T. / Panepucci, E. / Kobilka, B. / Diederichs, K. / Wang, M. / Caffrey, M.
History
DepositionAug 10, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jan 13, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 2, 2016Group: Database references
Revision 1.2Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
D: Diacylglycerol kinase
E: Diacylglycerol kinase
F: Diacylglycerol kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,25822
Polymers85,2276
Non-polymers5,03116
Water75742
1
A: Diacylglycerol kinase
B: Diacylglycerol kinase
C: Diacylglycerol kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,38715
Polymers42,6133
Non-polymers3,77412
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8260 Å2
ΔGint-83 kcal/mol
Surface area16080 Å2
MethodPISA
2
D: Diacylglycerol kinase
E: Diacylglycerol kinase
F: Diacylglycerol kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,8717
Polymers42,6133
Non-polymers1,2584
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7160 Å2
ΔGint-80 kcal/mol
Surface area14260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.320, 91.340, 143.360
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 14204.451 Da / Num. of mol.: 6 / Mutation: A41C, C46A, I53V, I70L, M96L, V107D and C113A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: dgkA, b4042, JW4002 / Production host: Escherichia coli (E. coli) / References: UniProt: P0ABN1, diacylglycerol kinase (ATP)
#2: Chemical
ChemComp-78M / (2S)-2,3-DIHYDROXYPROPYL(7Z)-PENTADEC-7-ENOATE / 7.8 MONOACYLGLYCEROL


Mass: 314.460 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C18H34O4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 42 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.89 Å3/Da / Density % sol: 57.49 %
Crystal growTemperature: 277 K / Method: lipidic cubic phase
Details: 3-6 %(v/v) MPD, 0.1 M NaCl, 60 mM Mg(CH3COO)2 and 50 mM Na3C6H5O7, pH 5.6
PH range: 5.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 18, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 24904 / % possible obs: 99.6 % / Redundancy: 6.23 % / Net I/σ(I): 7.71
Reflection shellResolution: 2.8→2.87 Å / Redundancy: 5.63 % / Mean I/σ(I) obs: 1.61 / % possible all: 98.9

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ze3

3ze3


Resolution: 2.8→45.67 Å / SU ML: 0.45 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 28.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2659 1249 5.02 %
Rwork0.2214 --
obs0.2236 24904 99.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.8→45.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4484 0 352 42 4878
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0044898
X-RAY DIFFRACTIONf_angle_d0.6436584
X-RAY DIFFRACTIONf_dihedral_angle_d16.7971741
X-RAY DIFFRACTIONf_chiral_restr0.024816
X-RAY DIFFRACTIONf_plane_restr0.002776
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.91210.35551380.27562569X-RAY DIFFRACTION99
2.9121-3.04460.37421400.26482603X-RAY DIFFRACTION100
3.0446-3.20510.31621330.25012598X-RAY DIFFRACTION100
3.2051-3.40580.31231390.24492600X-RAY DIFFRACTION100
3.4058-3.66870.27741380.2212598X-RAY DIFFRACTION99
3.6687-4.03770.28081380.20062612X-RAY DIFFRACTION100
4.0377-4.62140.18841380.17162636X-RAY DIFFRACTION99
4.6214-5.82060.23681400.2322682X-RAY DIFFRACTION100
5.8206-45.67610.26241450.22722757X-RAY DIFFRACTION99

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