PDB-6ohm: Structure of tungstate bound human Phospholipase D2 catalytic domain

ID or keywords:

Entry

Database: PDB / ID: 6ohm

Title

Structure of tungstate bound human Phospholipase D2 catalytic domain

Components

Phospholipase D2

Keywords

HYDROLASE / phosphodiesterase / HKD motif

Function / homology

Function and homology information

Synthesis of PG / phosphatidic acid biosynthetic process / synaptic vesicle recycling / Synthesis of PA / phospholipase D / phospholipid catabolic process / phospholipase D activity / regulation of vesicle-mediated transport / small GTPase-mediated signal transduction / Fc-gamma receptor signaling pathway involved in phagocytosis ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 1.895 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	Mar 13, 2024	Group: Data collection / Database references / Derived calculations Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	6ohm.cif.gz	495 KB	Display	PDBx/mmCIF format
PDB format	pdb6ohm.ent.gz	404.2 KB	Display	PDB format
PDBx/mmJSON format	6ohm.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	6ohm_validation.pdf.gz	1.4 MB	Display	wwPDB validaton report
Full document	6ohm_full_validation.pdf.gz	1.5 MB	Display
Data in XML	6ohm_validation.xml.gz	52.3 KB	Display
Data in CIF	6ohm_validation.cif.gz	77.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/oh/6ohm ftp://data.pdbj.org/pub/pdb/validation_reports/oh/6ohm	HTTPS FTP

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Related structure data

Related structure data	6ohoC 6ohpC 6ohqC 6ohrC 6ohsC C: citing same article (ref.)
Similar structure data	1cxp-2 6ohq-2 5fiw-2 1d7w-3 5fiw-1 5msp-d 6ohp-1 4dl1-8 7bjv-1 7lan-3 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) #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

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

1

A: Phospholipase D2

hetero molecules

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

2

B: Phospholipase D2

hetero molecules

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

Unit cell

Length a, b, c (Å)	92.515, 132.242, 107.089
Angle α, β, γ (deg.)	90.00, 111.45, 90.00
Int Tables number	5
Space group name H-M	C121

Components on special symmetry positions

ID	Model	Components
1	1	B-1526- 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-WO4 / TUNGSTATE(VI)ION Mass: 247.838 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: WO₄ / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO₄
#4: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₃H₈O₃
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 998 / 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: 2.09 Å³/Da / Density % sol: 41.22 %
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: 1.2 Å
Detector	Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Aug 27, 2015
Radiation	Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.2 Å / Relative weight: 1
Reflection	Resolution: 1.895→50 Å / Num. obs: 94443 / % possible obs: 100 % / Redundancy: 6.7 % / CC_1/2: 0.99 / Net I/σ(I): 12.2
Reflection shell	Resolution: 1.895→1.96 Å / Num. unique obs: 9136

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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:

SAD / Resolution: 1.895→48.55 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.81

	R_factor	Num. reflection	% reflection
R_free	0.2057	4712	4.99 %
R_work	0.1824	-	-
obs	0.1835	94443	99.52 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.895→48.55 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	9343	0	76	998	10417

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.003	9647
X-RAY DIFFRACTION	f_angle_d	0.608	13098
X-RAY DIFFRACTION	f_dihedral_angle_d	4.485	5666
X-RAY DIFFRACTION	f_chiral_restr	0.044	1433
X-RAY DIFFRACTION	f_plane_restr	0.005	1660

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 (%)
1.8947-1.9163	0.3277	147	0.2995	2599	X-RAY DIFFRACTION	86
1.9163-1.9388	0.2789	155	0.2706	2959	X-RAY DIFFRACTION	100
1.9388-1.9625	0.305	173	0.2635	3024	X-RAY DIFFRACTION	100
1.9625-1.9873	0.2687	151	0.2528	2984	X-RAY DIFFRACTION	100
1.9873-2.0135	0.2882	167	0.2474	3002	X-RAY DIFFRACTION	100
2.0135-2.041	0.2664	172	0.2245	2933	X-RAY DIFFRACTION	100
2.041-2.0702	0.272	180	0.2201	3020	X-RAY DIFFRACTION	100
2.0702-2.1011	0.2356	175	0.2108	3004	X-RAY DIFFRACTION	100
2.1011-2.1339	0.2127	182	0.2055	2935	X-RAY DIFFRACTION	100
2.1339-2.1689	0.2366	157	0.2046	2976	X-RAY DIFFRACTION	100
2.1689-2.2063	0.2101	154	0.2046	3004	X-RAY DIFFRACTION	100
2.2063-2.2464	0.2294	127	0.1925	3025	X-RAY DIFFRACTION	100
2.2464-2.2896	0.1976	158	0.1908	2996	X-RAY DIFFRACTION	100
2.2896-2.3364	0.2273	145	0.1931	2998	X-RAY DIFFRACTION	100
2.3364-2.3872	0.2374	156	0.196	3006	X-RAY DIFFRACTION	100
2.3872-2.4427	0.2144	156	0.1949	3033	X-RAY DIFFRACTION	100
2.4427-2.5038	0.2343	193	0.1897	2962	X-RAY DIFFRACTION	100
2.5038-2.5715	0.2288	163	0.1862	2987	X-RAY DIFFRACTION	100
2.5715-2.6471	0.221	147	0.1848	2997	X-RAY DIFFRACTION	100
2.6471-2.7326	0.1896	149	0.1796	3028	X-RAY DIFFRACTION	100
2.7326-2.8302	0.202	138	0.1885	3018	X-RAY DIFFRACTION	100
2.8302-2.9435	0.2141	155	0.1794	2999	X-RAY DIFFRACTION	100
2.9435-3.0775	0.2297	171	0.1813	3009	X-RAY DIFFRACTION	100
3.0775-3.2397	0.2186	153	0.1783	3020	X-RAY DIFFRACTION	100
3.2397-3.4426	0.1722	189	0.1679	2953	X-RAY DIFFRACTION	100
3.4426-3.7084	0.1358	142	0.1534	3049	X-RAY DIFFRACTION	100
3.7084-4.0814	0.1518	140	0.1433	3013	X-RAY DIFFRACTION	100
4.0814-4.6715	0.1562	130	0.1366	3058	X-RAY DIFFRACTION	100
4.6715-5.884	0.1743	130	0.1588	3060	X-RAY DIFFRACTION	100
5.884-48.5656	0.2094	157	0.1894	3080	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	0.7644	0.0014	0.1726	0.6602	0.0448	1.2611	-0.0315	0.0745	-0.047	-0.0575	0.0005	0.0239	0.0691	-0.0814	0.0192	0.1272	-0.0203	0.0144	0.1304	-0.017	0.139	23.4875	93.1767	-4.8354
2	0.872	0.4075	-0.0718	1.5781	0.0127	1.1326	-0.0327	0.168	0.1299	-0.1655	0.0496	0.1224	-0.1316	-0.0962	-0.0084	0.1231	0.0051	0.0116	0.1562	-0.0119	0.1252	24.1158	105.1649	-7.787
3	0.3677	0.1718	0.1692	0.8636	0.4305	0.8502	-0.0169	-0.0332	0.0371	0.0726	-0.0357	0.0695	-0.003	-0.0304	0.0433	0.129	-0.0065	0.0171	0.165	-0.0115	0.172	22.0217	103.6628	14.538
4	0.3825	0.0223	-0.0934	0.8228	-0.0531	0.5816	0.0055	-0.0121	0.1134	0.0215	0.0032	-0.0287	-0.1282	0.005	0.0117	0.1499	-0.0134	0.0095	0.1577	-0.0197	0.1824	29.9473	117.3203	10.95
5	1.2362	0.455	0.8118	0.3397	0.2848	1.2744	0.2663	-0.257	-0.2759	0.2259	-0.1651	-0.1176	0.3888	-0.2646	-0.044	0.2573	-0.0774	-0.0253	0.2003	0.0403	0.1883	-3.4307	62.8983	50.9525
6	0.9817	0.2407	0.5397	1.6978	0.5554	2.1516	0.1882	-0.282	-0.0416	0.3892	-0.1129	-0.1681	0.1937	-0.095	-0.0413	0.2191	-0.0777	-0.0256	0.2293	0.0359	0.1356	3.0029	71.6733	59.3144
7	0.8691	0.1503	0.3904	1.1614	0.245	1.7582	0.0684	0.0159	-0.0271	0.0508	-0.0062	-0.1289	-0.0494	0.0839	-0.0352	0.1001	0.0143	0.0155	0.1233	-0.0026	0.1385	3.6709	74.208	36.3148
8	0.8611	0.5531	0.5771	1.8141	0.3892	2.0998	-0.1847	0.005	0.1945	-0.1786	0.0667	-0.074	-0.6935	-0.0995	0.0958	0.3459	0.0588	0.0102	0.1449	-0.0128	0.1884	-1.2993	91.3254	37.4286

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 316 through 461 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 462 through 569 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 570 through 716 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 717 through 933 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 315 through 373 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 374 through 569 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 570 through 803 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 804 through 933 )

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