PDB-5dwk: Diacylglycerol Kinase solved by multi crystal multi orientation n...

ID or keywords:

Entry

Database: PDB / ID: 5dwk

Title

Diacylglycerol Kinase solved by multi crystal multi orientation native SAD

Components

Diacylglycerol kinase

Keywords

TRANSFERASE / native SAD / DAGK / multi crystal / multi orientation

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

Biological species

Escherichia coli (E. coli)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.601 Å

Authors

Weinert, T. / Olieric, V. / Finke, A.D. / Li, D. / Caffrey, M. / Wang, M.

Citation

Journal: Acta Crystallogr D Struct Biol / Year: 2016
Title: Data-collection strategy for challenging native SAD phasing.
Authors: Olieric, V. / Weinert, T. / Finke, A.D. / Anders, C. / Li, D. / Olieric, N. / Borca, C.N. / Steinmetz, M.O. / Caffrey, M. / Jinek, M. / Wang, M.

History

Deposition	Sep 22, 2015	Deposition site: RCSB / Processing site: PDBE
Revision 1.0	Mar 23, 2016	Provider: repository / Type: Initial release
Revision 1.1	May 8, 2024	Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5dwk.cif.gz	238.9 KB	Display	PDBx/mmCIF format
PDB format	pdb5dwk.ent.gz	195 KB	Display	PDB format
PDBx/mmJSON format	5dwk.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	5dwk_validation.pdf.gz	2.2 MB	Display	wwPDB validaton report
Full document	5dwk_full_validation.pdf.gz	2.3 MB	Display
Data in XML	5dwk_validation.xml.gz	24.7 KB	Display
Data in CIF	5dwk_validation.cif.gz	32.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/dw/5dwk ftp://data.pdbj.org/pub/pdb/validation_reports/dw/5dwk	HTTPS FTP

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Related structure data

Related structure data	5fq5C C: citing same article (ref.)
Similar structure data	4brb-1 3ze3-2 2r9l-1 5d56-1 5hnf-d 6tto-d 4yhg-1 2ron-d 4uwt-d 2a94-d Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Diacylglycerol kinase

B: Diacylglycerol kinase

C: Diacylglycerol kinase

D: Diacylglycerol kinase

E: Diacylglycerol kinase

F: Diacylglycerol kinase

hetero molecules

89.7 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Diacylglycerol kinase

B: Diacylglycerol kinase

D: Diacylglycerol kinase

hetero molecules

defined by author&software
45.5 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: Diacylglycerol kinase

E: Diacylglycerol kinase

F: Diacylglycerol kinase

hetero molecules

defined by author&software
44.2 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	75.290, 91.570, 143.720
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

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Protein , 1 types, 6 molecules ABCDEF

#1: Protein	Diacylglycerol kinase / DAGK / Diglyceride kinase / DGK Mass: 14204.451 Da / Num. of mol.: 6 / Fragment: UNP residues 2-122 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: dgkA, b4042, JW4002 / Plasmid: PTRCHISB_DGKA_DELTA7 / Production host: Escherichia coli (E. coli) / Strain (production host): Wh1061 / References: UniProt: P0ABN1, diacylglycerol kinase (ATP)

#1: Protein

Diacylglycerol kinase / DAGK / Diglyceride kinase / DGK

Mass: 14204.451 Da / Num. of mol.: 6 / Fragment: UNP residues 2-122
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Escherichia coli (E. coli) / Strain: K12 / Gene: dgkA, b4042, JW4002 / Plasmid: PTRCHISB_DGKA_DELTA7 / Production host:

Escherichia coli (E. coli) / Strain (production host): Wh1061 / References: UniProt: P0ABN1, diacylglycerol kinase (ATP)

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Non-polymers , 7 types, 53 molecules

#2: Chemical	ChemComp-78N / (2R)-2,3-DIHYDROXYPROPYL(7Z)-PENTADEC-7-ENOATE / 7.8 MONOACYLGLYCEROL (2R) Mass: 314.460 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C₁₈H₃₄O₄
#3: Chemical	ChemComp-78M / (2S)-2,3-DIHYDROXYPROPYL(7Z)-PENTADEC-7-ENOATE / 7.8 MONOACYLGLYCEROL Mass: 314.460 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₁₈H₃₄O₄
#4: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#6: Chemical	ChemComp-CIT / CITRIC ACID Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₆H₈O₇
#7: Chemical	ChemComp-ACT / ACETATE ION Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₃O₂
#8: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 36 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION

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Sample preparation

Crystal	Density Matthews: 2.91 Å³/Da / Density % sol: 57.68 %
Crystal grow	Temperature: 277 K / Method: lipidic cubic phase / pH: 5.6 Details: 3-5 %(V/V) 2-METHYL-2, 4-PENTANEDIOL, 0.1 M SODIUM CHLORIDE, 0.06 M MAGNESIUM ACETATE, 0.1 M SODIUM CITRATE/HCL PH 5.6. CRYSTALLIZED USING THE IN MESO (LIPIDIC CUBIC PHASE) METHOD AT 4 ...Details: 3-5 %(V/V) 2-METHYL-2, 4-PENTANEDIOL, 0.1 M SODIUM CHLORIDE, 0.06 M MAGNESIUM ACETATE, 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.

Crystal

Density Matthews: 2.91 Å³/Da / Density % sol: 57.68 %

Crystal grow

Temperature: 277 K / Method: lipidic cubic phase / pH: 5.6
Details: 3-5 %(V/V) 2-METHYL-2, 4-PENTANEDIOL, 0.1 M SODIUM CHLORIDE, 0.06 M MAGNESIUM ACETATE, 0.1 M SODIUM CITRATE/HCL PH 5.6. CRYSTALLIZED USING THE IN MESO (LIPIDIC CUBIC PHASE) METHOD AT 4 ...

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 2.0664 Å
Detector	Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Jun 14, 2013
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 2.0664 Å / Relative weight: 1
Reflection	Resolution: 2.6→50 Å / Num. obs: 58770 / % possible obs: 99.6 % / Redundancy: 142.9 % / R_merge(I) obs: 0.221 / Net I/σ(I): 36.46
Reflection shell	Resolution: 2.6→2.67 Å / Redundancy: 55.85 % / R_merge(I) obs: 1.13 / Mean I/σ(I) obs: 4.18 / % possible all: 96.5

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Processing

Software

Name	Version	Classification
XDS		data reduction
XSCALE		data scaling
SHELXDE		phasing
PHENIX	(dev_2067: ???)	refinement

Refinement

Method to determine structure:

SAD / Resolution: 2.601→45.785 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.93 / Phase error: 23.79 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2453	2935	5 %
R_work	0.2014	-	-
obs	0.2036	58677	99.53 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 2.601→45.785 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4238	0	305	36	4579

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.004	4592
X-RAY DIFFRACTION	f_angle_d	0.717	6189
X-RAY DIFFRACTION	f_dihedral_angle_d	12.013	2693
X-RAY DIFFRACTION	f_chiral_restr	0.039	785
X-RAY DIFFRACTION	f_plane_restr	0.002	728

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
2.6012-2.6439	0.2597	136	0.2119	2535	X-RAY DIFFRACTION	96
2.6439-2.6895	0.2774	143	0.1965	2648	X-RAY DIFFRACTION	98
2.6895-2.7384	0.2288	138	0.1825	2622	X-RAY DIFFRACTION	99
2.7384-2.791	0.2372	143	0.1847	2673	X-RAY DIFFRACTION	100
2.791-2.848	0.2566	142	0.1883	2627	X-RAY DIFFRACTION	100
2.848-2.9099	0.2574	140	0.1839	2690	X-RAY DIFFRACTION	100
2.9099-2.9776	0.2577	141	0.1762	2643	X-RAY DIFFRACTION	100
2.9776-3.052	0.2408	143	0.179	2692	X-RAY DIFFRACTION	100
3.052-3.1345	0.2174	133	0.1892	2657	X-RAY DIFFRACTION	100
3.1345-3.2268	0.2353	138	0.185	2644	X-RAY DIFFRACTION	100
3.2268-3.3309	0.2204	140	0.1881	2668	X-RAY DIFFRACTION	100
3.3309-3.4499	0.2859	137	0.2062	2697	X-RAY DIFFRACTION	100
3.4499-3.588	0.2861	135	0.2053	2697	X-RAY DIFFRACTION	100
3.588-3.7512	0.3295	143	0.27	2621	X-RAY DIFFRACTION	99
3.7512-3.9489	0.2492	141	0.2177	2675	X-RAY DIFFRACTION	100
3.9489-4.1961	0.2457	140	0.1694	2659	X-RAY DIFFRACTION	100
4.1961-4.5198	0.2105	141	0.1589	2656	X-RAY DIFFRACTION	100
4.5198-4.9742	0.2182	140	0.1893	2671	X-RAY DIFFRACTION	100
4.9742-5.6928	0.2115	144	0.2205	2671	X-RAY DIFFRACTION	100
5.6928-7.1679	0.2811	142	0.2582	2651	X-RAY DIFFRACTION	100
7.1679-45.7921	0.2262	135	0.2095	2645	X-RAY DIFFRACTION	99

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°²)	L12 (°²)	L13 (°²)	L22 (°²)	L23 (°²)	L33 (°²)	S11 (Å °)	S12 (Å °)	S13 (Å °)	S21 (Å °)	S22 (Å °)	S23 (Å °)	S31 (Å °)	S32 (Å °)	S33 (Å °)	T11 (Å²)	T12 (Å²)	T13 (Å²)	T22 (Å²)	T23 (Å²)	T33 (Å²)	Origin x (Å)	Origin y (Å)	Origin z (Å)
1	4.9233	-1.3315	-2.1333	4.2455	1.179	1.9818	-0.3486	-0.2381	-0.3551	0.7056	0.1863	-0.1965	0.6462	0.559	-0.0895	0.4763	0.0802	0.0223	0.301	0.0023	0.6648	59.0736	53.0317	79.4334
2	0.8148	0.7907	0.8354	2.6393	3.374	4.2031	-0.0749	-0.055	-0.0678	0.3629	-0.099	0.0166	0.642	-0.06	0.1546	0.2919	0.0637	-0.0106	0.3003	-0.0466	0.5425	53.3368	62.2351	85.1547
3	2.4891	-0.2367	-0.6146	3.2105	1.4385	5.3151	-0.0399	0.0995	-0.1598	0.3143	0.0912	0.1154	0.8077	-0.4421	-0.0133	0.3132	-0.0529	0.0347	0.1826	0.013	0.5428	44.4924	59.0371	86.9163
4	2.5882	0.5441	1.1814	1.3625	-0.6521	6.1147	-0.241	-0.4122	-1.1535	-0.0323	0.4137	0.5901	1.0508	0.3933	-0.4072	0.4967	0.0337	0.0263	0.3767	0.0718	0.5098	38.4892	57.524	94.2324
5	1.0867	-0.7859	-0.4703	1.5163	-0.8892	1.9458	-0.1031	0.087	-0.1101	0.083	-0.1134	0.1761	-0.1724	-0.1837	0.2229	0.2623	-0.0057	0.0003	0.3108	-0.0326	0.5192	38.7291	67.2035	81.1417
6	7.3034	2.4904	7.0398	7.1969	6.1763	2.0584	-0.259	0.4536	0.3337	-0.7955	-0.2094	0.4618	-1.5947	0.6583	0.6007	0.399	-0.0415	-0.0097	0.236	0.0768	0.5197	43.7289	76.4979	79.2511
7	6.0971	-4.8231	-2.3954	4.15	0.5381	7.2594	-0.1376	-0.122	0.5779	-0.5392	0.1876	-0.2895	0.1096	-0.3985	-0.0866	0.3782	-0.0498	0.0136	0.2271	-0.0064	0.4986	76.8457	54.4651	53.4536
8	1.4664	0.2463	-0.9221	2.2564	3.7669	7.6877	-0.1019	-0.0578	0.0208	0.1564	-0.0534	-0.042	0.4031	0.309	0.0589	0.352	0.018	0.0182	0.1915	-0.0285	0.5003	69.9763	48.5601	64.7588
9	4.5099	4.1414	-0.0458	4.8107	1.4235	2.9139	-1.0213	1.7299	0.1167	0.2729	3.002	0.0124	-0.0735	0.7754	-2.222	0.7806	0.0473	-0.0408	1.1459	-0.1466	1.0965	60.3444	43.9547	37.7231
10	2.9627	-1.5899	-2.4516	3.6814	2.3455	9.1678	-0.3416	-0.1314	-0.3077	0.5417	-0.1845	0.4522	0.8705	-1.2964	0.2592	0.4759	-0.069	0.0425	0.2985	-0.002	0.6704	62.2423	41.6809	65.2494
11	8.4165	1.7675	4.9214	6.1644	3.8414	5.4918	0.3775	0.0513	2.3578	-0.5558	-1.2213	0.6401	0.0531	-0.2447	0.1934	0.6443	0.0966	0.2671	0.3523	-0.0305	1.1057	56.794	79.1466	66.5867
12	2.3377	-1.0387	-1.1039	1.9022	0.7112	4.2568	0.0678	-0.0059	0.1152	0.2105	0.02	-0.1372	-0.7068	1.0331	0.2757	0.3793	-0.0632	0.0265	0.2163	-0.0335	0.5058	53.5957	73.7161	82.6968
13	2.0338	-0.2645	-1.8496	1.9399	-0.3518	2.4936	0.0646	-0.3811	0.0773	0.1983	0.0158	-0.2547	0.0632	0.7951	0.1931	0.2507	-0.0241	-0.0363	0.4191	-0.0509	0.5583	60.9047	67.5558	82.5989
14	2.0001	7.75	7.8594	5.6834	6.2188	8.3982	0.8261	-0.5754	0.664	1.0228	-1.0159	3.2033	1.0339	-1.1383	0.1004	0.6412	-0.1594	-0.1108	0.2907	0.0738	1.5709	59.3429	26.9708	67.2041
15	6.3534	1.8798	3.8803	4.4806	3.6804	4.0054	0.7512	-2.2735	-1.5207	2.8147	-0.0974	0.598	1.7752	-2.6189	-0.736	1.2314	-0.2765	0.2435	0.9841	0.1891	1.0775	61.3046	28.3859	79.543
16	0.7987	-0.3179	0.8906	1.1375	2.3434	7.7148	0.0929	0.0399	-0.1144	0.0482	0.1305	0.0844	1.4642	-0.4386	0.0702	0.5245	-0.0027	-0.0247	0.2945	-0.0223	0.5637	68.7836	33.965	53.7475
17	2.4474	0.4459	-0.5142	5.1163	-4.8689	4.9085	-0.2758	-0.2562	-0.5382	0.6657	-0.1559	-0.0802	1.786	0.7138	0.6314	1.0945	0.1602	0.0513	0.2714	0.045	0.6465	73.9845	26.6886	66.4151
18	0.6566	-0.0736	-1.5998	2.1494	0.9552	4.1473	-1.1313	-0.7791	-0.1952	0.8865	0.2963	-1.938	0.7425	1.7309	0.1632	0.75	0.4798	-0.1868	1.0117	-0.2814	2.2384	87.9608	31.4895	72.1794
19	1.7929	0.8636	-2.4106	1.6594	1.1987	8.5579	-0.152	0.2562	-0.1712	-0.0657	0.2065	-0.1469	0.6304	1.0937	-0.1345	0.4377	0.1401	0.0139	0.3668	-0.1052	0.6493	78.8757	37.6745	53.7895
20	6.3696	-0.0211	4.2383	4.822	-4.2288	6.4719	0.2435	-0.3046	-0.3001	0.1994	-0.1143	-0.1182	-0.6679	1.193	0.1499	0.2261	0.008	0.0328	0.3484	-0.0385	0.5258	81.1952	45.2441	65.7709

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 25 through 51 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 52 through 82 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 83 through 119 )
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 7 through 27 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 28 through 85 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 86 through 123 )
7	X-RAY DIFFRACTION	7	chain 'C' and (resid 15 through 28 )
8	X-RAY DIFFRACTION	8	chain 'C' and (resid 29 through 82 )
9	X-RAY DIFFRACTION	9	chain 'C' and (resid 83 through 87 )
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 88 through 120 )
11	X-RAY DIFFRACTION	11	chain 'D' and (resid 34 through 51 )
12	X-RAY DIFFRACTION	12	chain 'D' and (resid 52 through 82 )
13	X-RAY DIFFRACTION	13	chain 'D' and (resid 83 through 120 )
14	X-RAY DIFFRACTION	14	chain 'E' and (resid 36 through 41 )
15	X-RAY DIFFRACTION	15	chain 'E' and (resid 42 through 51 )
16	X-RAY DIFFRACTION	16	chain 'E' and (resid 52 through 92 )
17	X-RAY DIFFRACTION	17	chain 'E' and (resid 93 through 119 )
18	X-RAY DIFFRACTION	18	chain 'F' and (resid 35 through 51 )
19	X-RAY DIFFRACTION	19	chain 'F' and (resid 52 through 90 )
20	X-RAY DIFFRACTION	20	chain 'F' and resid ' 66 ' and name ' SD ' and altloc ' '

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Protein , 1 types, 6 molecules ABCDEF

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Non-polymers , 7 types, 53 molecules

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