PDB-6oho: Structure of human Phospholipase D2 catalytic domain

ID or keywords:

Entry

Database: PDB / ID: 6oho

Title

Structure of human Phospholipase D2 catalytic domain

Components

Phospholipase D2

Keywords

HYDROLASE /

phosphodiesterase / HKD motif

Function / homology

Function and homology information

Synthesis of PG / N-acylphosphatidylethanolamine-specific phospholipase D activity /

phospholipase D / phosphatidic acid biosynthetic process /

synaptic vesicle recycling / Synthesis of PA /

phospholipase D activity / phospholipid catabolic process / regulation of vesicle-mediated transport / small GTPase-mediated signal transduction ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2 Å

Authors

Metrick, C.M. / Chodaparambil, J.V.

Citation

Journal: Nat.Chem.Biol. / Year: 2020
Title: Human PLD structures enable drug design and characterization of isoenzyme selectivity.
Authors: Metrick, C.M. / Peterson, E.A. / Santoro, J.C. / Enyedy, I.J. / Murugan, P. / Chen, T. / Michelsen, K. / Cullivan, M. / Spilker, K.A. / Kumar, P.R. / May-Dracka, T.L. / Chodaparambil, J.V.

History

Deposition	Apr 6, 2019	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Feb 19, 2020	Provider: repository / Type: Initial release
Revision 1.1	Apr 1, 2020	Group: Database references / Category: citation Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2	Oct 11, 2023	Group: 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

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	6oho.cif.gz	492.1 KB	Display	PDBx/mmCIF format
PDB format	pdb6oho.ent.gz	402.7 KB	Display	PDB format
PDBx/mmJSON format	6oho.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/oh/6oho ftp://data.pdbj.org/pub/pdb/validation_reports/oh/6oho	HTTPS FTP

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Related structure data

Related structure data	6ohmSC 6ohpC 6ohqC 6ohrC 6ohsC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	6ohs-1 6ohs-2 6ohp-4 6ohp-2 6ohp-3 6ohp-1 6ohs-4 5yj6-d 1dnu-2 1l2a-6 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
Related items in Molecule of the Month	#239 - Nov 2019 Phospholipase A2 similarity (1) #92 - Aug 2007 Anabolic Steroids similarity (1) #127 - Jul 2010 Crystallins similarity (1) #174 - Jun 2014 GFP-like Proteins similarity (1) #89 - May 2007 Aconitase and Iron Regulatory Protein 1 similarity (1) #35 - Nov 2002 Ferritin and Transferrin similarity (2) #214 - Oct 2017 Chimeric Antigen Receptors similarity (1) #245 - May 2020 Spliceosomes similarity (1) #136 - Apr 2011 Nanobodies similarity (1) #21 - Sep 2001 Antibodies similarity (1) #148 - Apr 2012 Ras Protein similarity (1)

PDB pages

PDBj /

wwPDB /

NCBI

Related items in Molecule of the Month

#239 - Nov 2019
Phospholipase A2
similarity (1)
#92 - Aug 2007
Anabolic Steroids
similarity (1)
#127 - Jul 2010
Crystallins
similarity (1)
#174 - Jun 2014
GFP-like Proteins
similarity (1)
#89 - May 2007
Aconitase and Iron Regulatory Protein 1
similarity (1)
#35 - Nov 2002
Ferritin and Transferrin
similarity (2)
#214 - Oct 2017
Chimeric Antigen Receptors
similarity (1)
#245 - May 2020
Spliceosomes
similarity (1)
#136 - Apr 2011
Nanobodies
similarity (1)
#21 - Sep 2001
Antibodies
similarity (1)
#148 - Apr 2012
Ras Protein
similarity (1)

Deposited unit

A: Phospholipase D2

B: Phospholipase D2

hetero molecules

148 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Phospholipase D2

hetero molecules

defined by author&software
74 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Phospholipase D2

hetero molecules

defined by author&software
74.2 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	91.705, 131.336, 107.294
Angle α, β, γ (deg.)	90.00, 111.77, 90.00
Int Tables number	5
Space group name H-M	C121

Components on special symmetry positions

ID	Model	Components
1	1	B-1222- HOH

#1: Protein	Phospholipase D2 / hPLD2 / Choline phosphatase 2 / PLD1C / Phosphatidylcholine-hydrolyzing phospholipase D2 Mass: 72846.781 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PLD2 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: O14939, phospholipase D
#2: Chemical	ChemComp-SO4 / SULFATE ION / Sulfate Mass: 96.063 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: SO₄
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Chemical	ChemComp-DTT / 2,3-DIHYDROXY-1,4-DITHIOBUTANE / 1,4-DITHIOTHREITOL / Dithiothreitol Mass: 154.251 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₄H₁₀O₂S₂
#5: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 394 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.06 Å³/Da / Density % sol: 40.27 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.7 Details: 0.2M ammonium sulfate, 20% PEG3350, 0.1M bis-tris pH 6.7

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.97 Å
Detector	Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 16, 2015
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97 Å / Relative weight: 1
Reflection	Resolution: 2→50 Å / Num. obs: 79191 / % possible obs: 99 % / Redundancy: 6.6 % / CC_1/2: 0.95 / Net I/σ(I): 6.3
Reflection shell	Resolution: 2→2.07 Å / Num. unique obs: 7826

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Processing

Software

Name	Version	Classification
PHENIX	(1.13_2998: ???)	refinement
XDS		data reduction
Aimless		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 6OHM

6ohm

Resolution: 2→48.57 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 24.39

	R_factor	Num. reflection	% reflection
R_free	0.2239	4141	5.23 %
R_work	0.1813	-	-
obs	0.1835	79166	99.66 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Refinement step

Cycle: LAST / Resolution: 2→48.57 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	9331	0	141	394	9866

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.005	9686
X-RAY DIFFRACTION	f_angle_d	0.747	13154
X-RAY DIFFRACTION	f_dihedral_angle_d	4.956	5658
X-RAY DIFFRACTION	f_chiral_restr	0.047	1436
X-RAY DIFFRACTION	f_plane_restr	0.005	1659

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 (%)
2-2.0227	0.347	130	0.3119	2451	X-RAY DIFFRACTION	99
2.0227-2.0465	0.332	125	0.2933	2508	X-RAY DIFFRACTION	100
2.0465-2.0715	0.3209	106	0.2774	2498	X-RAY DIFFRACTION	100
2.0715-2.0977	0.2983	138	0.2715	2510	X-RAY DIFFRACTION	99
2.0977-2.1253	0.3329	132	0.2571	2492	X-RAY DIFFRACTION	99
2.1253-2.1544	0.2739	145	0.254	2476	X-RAY DIFFRACTION	100
2.1544-2.1852	0.2859	168	0.2521	2462	X-RAY DIFFRACTION	100
2.1852-2.2178	0.3108	170	0.2529	2461	X-RAY DIFFRACTION	100
2.2178-2.2525	0.3022	161	0.2351	2444	X-RAY DIFFRACTION	99
2.2525-2.2894	0.2599	145	0.231	2526	X-RAY DIFFRACTION	99
2.2894-2.3289	0.2666	136	0.2262	2456	X-RAY DIFFRACTION	100
2.3289-2.3712	0.2434	137	0.2251	2503	X-RAY DIFFRACTION	100
2.3712-2.4168	0.3104	121	0.225	2520	X-RAY DIFFRACTION	100
2.4168-2.4662	0.3063	138	0.2188	2465	X-RAY DIFFRACTION	100
2.4662-2.5198	0.2739	135	0.2148	2514	X-RAY DIFFRACTION	100
2.5198-2.5784	0.2628	129	0.2053	2551	X-RAY DIFFRACTION	100
2.5784-2.6429	0.2256	130	0.1972	2466	X-RAY DIFFRACTION	100
2.6429-2.7143	0.2523	133	0.1868	2524	X-RAY DIFFRACTION	100
2.7143-2.7942	0.2489	147	0.1833	2496	X-RAY DIFFRACTION	100
2.7942-2.8844	0.2453	147	0.1876	2504	X-RAY DIFFRACTION	100
2.8844-2.9875	0.2267	155	0.1867	2502	X-RAY DIFFRACTION	100
2.9875-3.107	0.244	131	0.1868	2488	X-RAY DIFFRACTION	100
3.107-3.2484	0.2251	125	0.1725	2532	X-RAY DIFFRACTION	100
3.2484-3.4196	0.1856	135	0.1649	2506	X-RAY DIFFRACTION	100
3.4196-3.6338	0.1858	129	0.1502	2542	X-RAY DIFFRACTION	100
3.6338-3.9143	0.1853	134	0.1432	2486	X-RAY DIFFRACTION	100
3.9143-4.308	0.1751	143	0.137	2524	X-RAY DIFFRACTION	100
4.308-4.9308	0.1529	143	0.1334	2517	X-RAY DIFFRACTION	100
4.9308-6.2103	0.213	146	0.1627	2526	X-RAY DIFFRACTION	100
6.2103-48.5845	0.2112	127	0.1718	2575	X-RAY DIFFRACTION	100

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	1.2631	0.3357	0.609	1.0213	0.1744	2.1331	-0.1017	0.1429	-0.0147	-0.2884	0.0746	-0.034	0.1598	-0.1075	0.0003	0.3377	-0.0539	0.055	0.2119	-0.0284	0.234	24.3875	7.1761	-6.0406
2	1.0406	-0.3739	-0.1489	1.8039	0.3241	1.3455	-0.1088	0.18	-0.0227	-0.4215	0.0744	-0.1731	-0.0379	-0.1455	0.0284	0.3207	-0.0438	0.009	0.2468	-0.0201	0.2008	24.5915	16.3886	-5.0031
3	0.8931	0.754	0.2906	2.842	-0.0876	1.4308	-0.0157	0.1838	0.1147	-0.2698	-0.0201	0.1601	0.0706	-0.1486	0.0031	0.2918	-0.0114	0.0622	0.3297	-0.0256	0.2494	21.4092	12.2945	-5.453
4	1.0351	0.3955	0.213	2.0825	0.5866	1.2503	-0.0649	-0.0876	0.1361	0.008	-0.0228	0.1242	-0.1051	-0.1824	0.1004	0.2397	0.0025	0.0139	0.266	-0.0201	0.2303	22.3751	21.517	17.5159
5	0.4147	0.142	-0.4467	1.3389	-0.1634	1.0403	0.0033	-0.0036	0.1267	-0.0465	0.0584	-0.02	-0.1606	-0.0497	-0.045	0.2603	-0.016	0.0133	0.2654	-0.0162	0.2936	29.1896	31.6313	10.9421
6	3.0999	0.8394	0.8272	2.0988	1.4785	2.6781	0.6268	-0.9795	-0.1934	0.612	-0.4719	-0.3126	0.5528	-0.4237	-0.0557	0.4392	-0.2772	-0.0695	0.5697	0.1588	0.252	-1.2541	-20.1207	57.3016
7	2.183	1.6605	1.0975	1.9862	0.9216	2.6282	0.4745	-0.7649	-0.146	0.4968	-0.3595	-0.3127	0.3962	-0.4063	0.0017	0.3073	-0.1641	-0.061	0.493	0.0743	0.2643	2.452	-14.9295	56.1212
8	1.9664	1.2685	0.9445	2.4369	1.0579	2.4268	0.4778	-0.8327	0.0944	0.7824	-0.4559	-0.2616	0.1414	-0.2387	-0.0421	0.3694	-0.1728	-0.0523	0.5637	0.0007	0.3214	1.9606	-9.7073	58.0363
9	2.0156	0.469	0.4767	2.0215	0.414	2.3928	0.3094	-0.2284	-0.4046	0.3013	-0.1373	-0.5471	0.3669	0.0901	-0.0541	0.2757	-0.0204	-0.0799	0.216	0.0756	0.3351	4.6935	-21.9355	41.4484
10	3.0175	0.1909	1.3285	1.9706	0.8084	3.6493	-0.1283	0.0561	0.0633	-0.1113	0.1844	-0.3111	-0.3812	0.3466	-0.0618	0.3074	-0.0188	0.0835	0.214	0.0345	0.3113	7.4161	-3.2454	31.3037
11	2.0069	0.1818	1.0685	2.3326	0.0971	1.8552	-0.0041	-0.162	0.1072	-0.0862	-0.0293	-0.1948	-0.1413	-0.1149	-0.0128	0.1721	0.0294	0.0429	0.1929	-0.0119	0.2144	-0.9708	-6.9549	35.665
12	2.1883	-1.2185	0.2439	2.7864	-0.5511	0.8432	-0.1107	-0.3135	0.3759	0.0345	0.0729	0.31	-0.3642	-0.5761	0.0534	0.2525	0.0917	0.0044	0.4038	-0.0205	0.3275	-16.2335	-5.8862	34.1987
13	1.8046	0.8978	1.2353	3.0814	0.9091	2.6607	-0.5599	-0.2875	0.5895	-0.4475	0.1781	-0.3985	-0.9083	-0.0499	0.185	0.6052	0.0792	-0.0549	0.2958	-0.1019	0.4786	3.1521	11.0409	38.2982

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 315 through 432 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 433 through 502 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 503 through 599 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 600 through 716 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 717 through 933 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 315 through 421 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 422 through 476 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 498 through 569 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 570 through 656 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 657 through 716 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 717 through 803 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 804 through 839 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 840 through 933 )

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