PDB-4r6w: Plasmodium falciparum phosphoethanolamine methyltransferase D128A...

ID or keywords:

Entry

Database: PDB / ID: 4r6w

Title

Plasmodium falciparum phosphoethanolamine methyltransferase D128A mutant in complex with S-adenosylhomocysteine and phosphocholine

Components

Phosphoethanolamine N-methyltransferase

Keywords

TRANSFERASE / methyltransferase

Function / homology

Function and homology information

: / phosphoethanolamine N-methyltransferase activity / phosphoethanolamine N-methyltransferase / phosphatidylcholine biosynthetic process / methylation / Golgi membrane / Golgi apparatus
Similarity search - Function

Biological species

Plasmodium falciparum (malaria parasite P. falciparum)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.5894 Å

Authors

Lee, S.G. / Jez, J.M.

Citation

Journal: J.Biol.Chem. / Year: 2014
Title: An Alternative Mechanism for the Methylation of Phosphoethanolamine Catalyzed by Plasmodium falciparum Phosphoethanolamine Methyltransferase.
Authors: Saen-Oon, S. / Lee, S.G. / Jez, J.M. / Guallar, V.

History

Deposition	Aug 26, 2014	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 8, 2014	Provider: repository / Type: Initial release
Revision 1.1	Oct 22, 2014	Group: Database references
Revision 1.2	Dec 24, 2014	Group: Database references
Revision 1.3	Sep 20, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4r6w.cif.gz	240.1 KB	Display	PDBx/mmCIF format
PDB format	pdb4r6w.ent.gz	193.1 KB	Display	PDB format
PDBx/mmJSON format	4r6w.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4r6w_validation.pdf.gz	974.2 KB	Display	wwPDB validaton report
Full document	4r6w_full_validation.pdf.gz	977.4 KB	Display
Data in XML	4r6w_validation.xml.gz	28.1 KB	Display
Data in CIF	4r6w_validation.cif.gz	43 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/r6/4r6w ftp://data.pdbj.org/pub/pdb/validation_reports/r6/4r6w	HTTPS FTP

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Related structure data

Related structure data	4r6xC 3uj7S 3uj6 3uj8 3uj9 3uja 3ujb S: Starting model for refinement C: citing same article (ref.)
Similar structure data	6mfi-d 3uj7-1 5swu-1 3uj8-d 1n57-d 1ons-d 4r6x-1 1fxu-d 2g18-8 3uj6-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: Phosphoethanolamine N-methyltransferase

B: Phosphoethanolamine N-methyltransferase

hetero molecules

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

1

A: Phosphoethanolamine N-methyltransferase

hetero molecules

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

2

B: Phosphoethanolamine N-methyltransferase

hetero molecules

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

Unit cell

Length a, b, c (Å)	77.171, 44.062, 89.147
Angle α, β, γ (deg.)	90.00, 108.09, 90.00
Int Tables number	3
Space group name H-M	P121

Components on special symmetry positions

ID	Model	Components
1	1	A-401- HOH
2	1	A-608- HOH
3	1	A-637- HOH
4	1	B-401- HOH
5	1	B-670- HOH

#1: Protein	Phosphoethanolamine N-methyltransferase Mass: 30111.012 Da / Num. of mol.: 2 / Mutation: D128A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum) Gene: PMT / Plasmid: pET-28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q6T755
#2: Chemical	ChemComp-PC / PHOSPHOCHOLINE Mass: 184.151 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₅H₁₅NO₄P
#3: Chemical	ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₄H₂₀N₆O₅S
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 694 / 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: 2.39 Å³/Da / Density % sol: 48.59 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 20% PEG-8000, 0.1 M sodium cacodylate, pH 6.5, 0.2 M sodium acetate, 20 mM tris(2-carboxyethyl)phosphine, 5 mM SAH, and 5 mM pCho, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.98 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 26, 2014
Radiation	Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.98 Å / Relative weight: 1
Reflection	Resolution: 1.589→30.394 Å / Num. all: 77182 / Num. obs: 76287 / % possible obs: 98.84 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0

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Processing

Software

Name	Version	Classification
HKL-3000		data collection
PHASER		phasing
PHENIX	(phenix.refine: 1.8.4_1496)	refinement
HKL-3000		data reduction
HKL-3000		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB entry 3UJ7

3uj7

Resolution: 1.5894→30.394 Å / SU ML: 0.14 / σ(F): 1.34 / Phase error: 19.14 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1877	3749	4.91 %	random
R_work	0.1593	-	-	-
obs	0.1607	76287	98.84 %	-
all	-	77182	-	-

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.5894→30.394 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4242	0	74	694	5010

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	4487
X-RAY DIFFRACTION	f_angle_d	1.026	6066
X-RAY DIFFRACTION	f_dihedral_angle_d	17.506	1749
X-RAY DIFFRACTION	f_chiral_restr	0.044	647
X-RAY DIFFRACTION	f_plane_restr	0.004	763

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 (%)
1.5894-1.6095	0.2348	122	0.2185	2128	X-RAY DIFFRACTION	79
1.6095-1.6307	0.239	148	0.2155	2707	X-RAY DIFFRACTION	100
1.6307-1.653	0.2577	145	0.2099	2620	X-RAY DIFFRACTION	100
1.653-1.6766	0.2597	147	0.2009	2717	X-RAY DIFFRACTION	100
1.6766-1.7016	0.22	118	0.194	2681	X-RAY DIFFRACTION	100
1.7016-1.7282	0.2362	137	0.1951	2661	X-RAY DIFFRACTION	100
1.7282-1.7566	0.2183	147	0.1893	2717	X-RAY DIFFRACTION	100
1.7566-1.7868	0.211	116	0.1935	2717	X-RAY DIFFRACTION	100
1.7868-1.8193	0.2418	141	0.1889	2714	X-RAY DIFFRACTION	100
1.8193-1.8543	0.2144	139	0.1839	2703	X-RAY DIFFRACTION	100
1.8543-1.8922	0.1872	121	0.1722	2703	X-RAY DIFFRACTION	100
1.8922-1.9333	0.1902	144	0.1721	2694	X-RAY DIFFRACTION	100
1.9333-1.9783	0.1922	158	0.1634	2686	X-RAY DIFFRACTION	100
1.9783-2.0277	0.183	142	0.1629	2710	X-RAY DIFFRACTION	100
2.0277-2.0825	0.1977	131	0.1565	2696	X-RAY DIFFRACTION	100
2.0825-2.1438	0.1908	113	0.1523	2725	X-RAY DIFFRACTION	100
2.1438-2.213	0.1843	160	0.1505	2708	X-RAY DIFFRACTION	100
2.213-2.2921	0.1889	143	0.1542	2687	X-RAY DIFFRACTION	100
2.2921-2.3838	0.2045	135	0.1563	2697	X-RAY DIFFRACTION	100
2.3838-2.4922	0.2136	143	0.1563	2715	X-RAY DIFFRACTION	100
2.4922-2.6236	0.2022	135	0.1656	2724	X-RAY DIFFRACTION	100
2.6236-2.7878	0.2004	128	0.1621	2726	X-RAY DIFFRACTION	99
2.7878-3.0029	0.1933	162	0.166	2695	X-RAY DIFFRACTION	99
3.0029-3.3048	0.2051	145	0.153	2716	X-RAY DIFFRACTION	99
3.3048-3.7822	0.1609	144	0.1361	2717	X-RAY DIFFRACTION	100
3.7822-4.7622	0.1231	142	0.1261	2750	X-RAY DIFFRACTION	99
4.7622-30.3996	0.1786	143	0.1688	2824	X-RAY DIFFRACTION	98

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	2.2588	0.7546	-0.131	3.4908	3.2141	9.3785	0.0066	-0.0762	0.2381	0.1327	-0.0259	0.2714	0.026	-0.2683	0.0124	0.1452	0.0107	0.0107	0.1234	0.0278	0.1952	4.9819	11.5134	26.1266
2	1.1286	0.2459	0.1074	2.704	-0.1504	0.9579	0.0084	0.1567	-0.0469	-0.1049	0.0119	0.0891	0.0373	-0.0384	-0.029	0.1416	-0.0026	-0.0123	0.1686	0.0012	0.1738	5.6157	-8.4165	24.3547
3	2.1946	2.1866	0.4777	4.8964	1.138	1.691	0.0135	0.1521	0.0822	-0.0462	0.1074	0.4134	-0.0349	-0.0286	-0.1325	0.1407	0.0179	0.0296	0.2227	0.0326	0.2397	-3.521	-1.4532	29.7624
4	1.3603	0.5772	-0.3658	2.275	-0.7404	0.9582	0.0447	-0.1041	-0.0077	0.1141	-0.0214	-0.0339	-0.0346	0.0163	-0.0273	0.1561	0.0006	-0.0018	0.1458	0.0081	0.1361	14.9592	-4.7927	35.4528
5	2.6663	1.4278	-2.5189	3.4393	0.7201	4.0159	0.0365	-0.1484	0.3988	-0.0413	0.0323	-0.1197	-0.1253	0.1851	-0.0808	0.1465	-0.0147	0.0106	0.1248	0.0148	0.1671	25.16	14.8935	24.3059
6	0.8356	-0.3864	-0.153	2.1553	-0.3816	0.7766	-0.02	-0.0636	0.0286	0.0516	-0.0326	-0.1564	0.0351	0.0422	0.0499	0.1359	0.0073	-0.0014	0.1519	0.0039	0.1336	25.0148	-3.3328	29.5253
7	4.3313	-2.8502	-0.1317	3.9258	0.0219	1.8398	0.2799	0.5459	0.0334	-0.4253	-0.2614	0.1562	0.0226	-0.1135	0.0073	0.1765	-0.0115	-0.0132	0.1738	0.0226	0.1348	8.7767	8.5715	9.1603
8	7.5356	-4.424	0.0308	5.0195	0.387	1.4133	0.0643	0.2753	0.458	-0.2568	-0.117	-0.1435	-0.1313	0.0566	0.0329	0.1867	-0.018	-0.0113	0.1693	0.0262	0.1546	14.3948	14.5484	13.2467
9	1.1301	1.7916	-1.0495	6.452	-3.4418	2.6694	-0.0267	-0.054	-0.106	-0.2	-0.0774	-0.1505	0.126	0.1137	0.1242	0.1186	0.0121	0.0223	0.1327	-0.0099	0.1325	23.0263	-2.6012	23.4838
10	1.3678	-0.4185	0.0688	3.1148	-3.0368	3.1358	0.0405	0.0574	0.2087	-0.1697	0.0161	-0.2331	0.0509	0.1665	-0.0663	0.1808	-0.0163	0.0203	0.1627	-0.0317	0.1975	56.9817	33.3069	17.7581
11	1.0637	0.2069	-0.0423	3.1563	0.5764	1.5518	0.0161	-0.1732	-0.0485	0.1938	0.022	-0.0717	0.0881	-0.0147	-0.0415	0.1344	0.0209	-0.0165	0.185	-0.0026	0.1871	54.3303	13.6461	21.0337
12	0.6252	0.3379	-0.2594	4.0699	-1.4614	1.449	0.0793	-0.1168	0.0306	-0.0165	-0.1101	-0.3403	-0.0187	0.2576	-0.0071	0.1491	0.0018	0.015	0.2129	-0.0212	0.2414	60.9793	17.4007	16.3608
13	1.7718	-0.2181	-0.0645	1.6332	0.2023	0.7174	-0.0127	0.1257	-0.072	-0.1417	0.013	-0.0462	-0.0311	0.0596	-0.0081	0.1691	-0.0076	0.0133	0.1471	-0.0037	0.141	50.935	16.6561	8.9182
14	2.6113	-0.9977	-2.0336	2.6909	-1.107	3.1671	-0.0676	0.212	0.4525	-0.0468	0.0289	0.1069	-0.1892	-0.1976	0.0034	0.1722	0.031	0.0003	0.1339	-0.0158	0.178	36.6864	36.8667	18.0111
15	1.361	0.3116	-0.1982	2.614	0.1141	0.9725	0.0329	0.0963	0.0084	-0.113	-0.0753	0.259	0.0226	-0.049	0.0144	0.1481	-0.0064	-0.0086	0.1682	-0.0117	0.1441	37.1219	18.621	13.0172
16	4.5088	2.7244	-0.3696	3.8552	0.093	2.045	0.1241	-0.408	-0.0181	0.3634	-0.1056	-0.1586	0.0332	0.1471	-0.0151	0.1895	0.0355	-0.0134	0.1831	-0.0231	0.1404	52.1008	30.5916	34.2007
17	7.7204	3.1848	0.3586	3.5982	0.0208	1.5709	0.0258	-0.1212	0.4306	0.15	-0.098	0.1961	-0.1709	-0.0604	0.0199	0.198	0.0212	0.0024	0.1647	-0.014	0.1454	46.7537	36.5075	29.8237
18	1.5813	-1.9285	-1.0681	7.7462	3.7462	3.3582	0.0221	0.08	-0.05	0.1728	-0.1	0.133	0.0965	-0.1921	0.1085	0.1091	-0.0037	0.0176	0.1463	0.009	0.1379	38.4778	19.7444	19.222

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 9 through 31 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 32 through 87 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 88 through 108 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 109 through 162 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 163 through 179 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 180 through 206 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 207 through 233 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 234 through 252 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 253 through 266 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 9 through 31 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 32 through 67 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 68 through 96 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 97 through 162 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 163 through 179 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 180 through 206 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 207 through 233 )
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 234 through 252 )
18	X-RAY DIFFRACTION	18	chain 'B' and (resid 253 through 266 )

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