PDB-5wp5: Arabidopsis thaliana phosphoethanolamine N-methyltransferase 2 (A...

ID or keywords:

Entry

Database: PDB / ID: 5wp5

Title

Arabidopsis thaliana phosphoethanolamine N-methyltransferase 2 (AtPMT2) in complex with SAH

Components

Phosphomethylethanolamine N-methyltransferase 2

Keywords

TRANSFERASE / Phosphoethanolamine N-Methyltransferase / AtPMT2

Function / homology

Function and homology information

phosphoethanolamine N-methyltransferase activity / : / phosphoethanolamine N-methyltransferase / phosphatidylcholine biosynthetic process / methylation / mRNA binding / cytoplasm
Similarity search - Function

Biological species

Arabidopsis thaliana (thale cress)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.5 Å

Authors

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

Funding support

United States, 2items

Organization	Grant number	Country
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	AI-097119	United States
Department of Energy (DOE, United States)	DE-AC02-06CH11357	United States

Citation

Journal: J. Biol. Chem. / Year: 2017
Title: Conformational changes in the di-domain structure of Arabidopsis phosphoethanolamine methyltransferase leads to active-site formation.
Authors: Lee, S.G. / Jez, J.M.

History

Deposition	Aug 3, 2017	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Nov 15, 2017	Provider: repository / Type: Initial release
Revision 1.1	Jan 10, 2018	Group: Database references / Category: citation Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2	Jan 17, 2018	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3	Dec 4, 2019	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4	Oct 4, 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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Download

PDBx/mmCIF format	5wp5.cif.gz	419.2 KB	Display	PDBx/mmCIF format
PDB format	pdb5wp5.ent.gz	337.7 KB	Display	PDB format
PDBx/mmJSON format	5wp5.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	5wp5_validation.pdf.gz	1.4 MB	Display	wwPDB validaton report
Full document	5wp5_full_validation.pdf.gz	1.4 MB	Display
Data in XML	5wp5_validation.xml.gz	47.1 KB	Display
Data in CIF	5wp5_validation.cif.gz	72.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/wp/5wp5 ftp://data.pdbj.org/pub/pdb/validation_reports/wp/5wp5	HTTPS FTP

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Related structure data

Related structure data	5wp4C 4krgS 4krhS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	1jke-5 6xxq-d 1yhc-2 6czo-d 1jc4-d 5inq-d 6je2-d 5uxv-d 6q6j-d 1bry-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: Phosphomethylethanolamine N-methyltransferase 2

B: Phosphomethylethanolamine N-methyltransferase 2

hetero molecules

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

1

A: Phosphomethylethanolamine N-methyltransferase 2

hetero molecules

defined by author
Evidence: gel filtration
56.9 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Phosphomethylethanolamine N-methyltransferase 2

hetero molecules

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

Unit cell

Length a, b, c (Å)	48.055, 90.224, 122.875
Angle α, β, γ (deg.)	90.00, 100.14, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Phosphomethylethanolamine N-methyltransferase 2 / AtPMEAMT Mass: 56115.285 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: NMT2, PMEAMT, At1g48600, T1N15.22/T1N15.23, T1N15_20 / Production host: Escherichia coli (E. coli) References: UniProt: Q944H0, Transferases; Transferring one-carbon groups; Methyltransferases
#2: Chemical	ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₁₄H₂₀N₆O₅S
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1175 / 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: 2.34 Å³/Da / Density % sol: 47.35 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, hanging drop / Details: 200 mM potassium formate, 20% w/v PEG3350

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Data collection

Diffraction	Mean temperature: 200 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.979 Å
Detector	Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 7, 2011
Radiation	Monochromator: Rosenbaum-Rock high-resolution double-crystal Si(111) Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.979 Å / Relative weight: 1
Reflection	Resolution: 1.5→30 Å / Num. obs: 162824 / % possible obs: 99.1 % / Redundancy: 4.6 % / Net I/σ(I): 37.4
Reflection shell	Highest resolution: 1.5 Å

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Processing

Software

Name	Version	Classification
PHENIX	1.8.1_1168	refinement
HKL-3000		data collection
PHASER		phasing
Coot		model building

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB entries 4KRG & 4KRH

4krg

4krh

Resolution: 1.5→30 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 17.52

	R_factor	Num. reflection	% reflection
R_free	0.1789	8177	5.02 %
R_work	0.16	-	-
obs	0.1609	162824	98.81 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.5→30 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7448	0	104	1175	8727

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	7834
X-RAY DIFFRACTION	f_angle_d	1.071	10579
X-RAY DIFFRACTION	f_dihedral_angle_d	18.717	3021
X-RAY DIFFRACTION	f_chiral_restr	0.076	1110
X-RAY DIFFRACTION	f_plane_restr	0.005	1366

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 (%)
1.4997-1.5168	0.2801	225	0.2461	4678	X-RAY DIFFRACTION	90
1.5168-1.5346	0.261	255	0.2213	5191	X-RAY DIFFRACTION	100
1.5346-1.5533	0.2339	286	0.2155	5226	X-RAY DIFFRACTION	100
1.5533-1.573	0.2403	275	0.2072	5173	X-RAY DIFFRACTION	100
1.573-1.5937	0.2267	272	0.1965	5229	X-RAY DIFFRACTION	100
1.5937-1.6155	0.21	270	0.1886	5179	X-RAY DIFFRACTION	100
1.6155-1.6386	0.2099	251	0.1813	5232	X-RAY DIFFRACTION	100
1.6386-1.6631	0.2011	267	0.1734	5204	X-RAY DIFFRACTION	100
1.6631-1.689	0.2014	290	0.1725	5159	X-RAY DIFFRACTION	100
1.689-1.7167	0.1927	259	0.1659	5258	X-RAY DIFFRACTION	100
1.7167-1.7463	0.2096	301	0.1692	5113	X-RAY DIFFRACTION	100
1.7463-1.7781	0.1807	245	0.1694	5300	X-RAY DIFFRACTION	100
1.7781-1.8123	0.2008	272	0.1593	5152	X-RAY DIFFRACTION	100
1.8123-1.8493	0.1839	281	0.157	5274	X-RAY DIFFRACTION	100
1.8493-1.8895	0.1916	284	0.1603	5172	X-RAY DIFFRACTION	100
1.8895-1.9334	0.1864	286	0.1568	5195	X-RAY DIFFRACTION	100
1.9334-1.9818	0.174	282	0.1641	5181	X-RAY DIFFRACTION	100
1.9818-2.0353	0.1932	258	0.163	5209	X-RAY DIFFRACTION	100
2.0353-2.0952	0.1774	292	0.1572	5236	X-RAY DIFFRACTION	100
2.0952-2.1628	0.1844	277	0.1546	5181	X-RAY DIFFRACTION	100
2.1628-2.2401	0.1734	298	0.1542	5161	X-RAY DIFFRACTION	100
2.2401-2.3297	0.1745	313	0.1552	5215	X-RAY DIFFRACTION	100
2.3297-2.4357	0.1916	286	0.1618	5205	X-RAY DIFFRACTION	100
2.4357-2.5641	0.1909	280	0.1645	5184	X-RAY DIFFRACTION	100
2.5641-2.7246	0.1875	286	0.1634	5156	X-RAY DIFFRACTION	99
2.7246-2.9348	0.1722	238	0.1622	5185	X-RAY DIFFRACTION	98
2.9348-3.2299	0.1684	263	0.161	5093	X-RAY DIFFRACTION	97
3.2299-3.6965	0.1681	243	0.1532	4858	X-RAY DIFFRACTION	92
3.6965-4.6544	0.1499	267	0.1377	5038	X-RAY DIFFRACTION	96
4.6544-30.0677	0.1731	275	0.1618	5010	X-RAY DIFFRACTION	94

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	3.537	3.0382	-1.0231	5.6384	-1.2837	3.3594	0.1233	-0.5337	-0.2324	0.5837	-0.0898	-0.347	0.4939	0.4912	-0.0221	0.3536	0.0135	-0.0435	0.3152	-0.0535	0.2243	-0.9899	3.8674	-0.4064
2	1.5775	0.3602	0.7857	2.4071	0.5502	2.7012	0.0996	-0.4635	0.1452	0.4149	0.046	-0.2873	-0.0743	0.6012	-0.0563	0.3569	-0.0644	-0.0701	0.4249	-0.1252	0.1472	1.9422	16.344	7.0009
3	1.3999	0.5609	-0.0299	2.1418	0.3391	3.0283	0.0767	-0.1427	0.0707	0.3116	-0.0565	0.0378	0.1111	-0.1328	-0.0438	0.1764	-0.0007	-0.0131	0.1994	-0.0324	0.1334	-7.6134	10.4193	-7.1423
4	1.565	0.4631	0.4151	1.7512	0.2073	2.5305	0.0325	0.0192	0.009	-0.0049	0.0499	-0.0114	0.0078	0.1297	-0.0572	0.173	-0.0027	-0.0073	0.148	-0.0246	0.1741	-2.887	15.9906	-17.1054
5	0.754	-0.0229	-0.29	1.067	-0.1419	0.6293	0.0378	0.0685	0.1289	-0.0584	-0.0156	-0.15	-0.0596	0.0527	-0.0187	0.1269	0.0051	0.0195	0.2245	0.0215	0.1902	5.5964	14.3045	-48.6629
6	3.1713	1.7696	-0.0106	3.424	0.1469	1.0416	-0.1335	0.4146	-0.286	-0.3704	0.0992	0.1054	0.1242	-0.0546	0.0122	0.2276	0.0188	0.0177	0.311	-0.0136	0.2248	1.1736	-2.1056	-61.1406
7	0.778	-0.0592	-0.4559	1.0952	-0.0995	1.3177	-0.0369	0.0838	-0.0388	-0.1904	-0.0238	-0.156	0.0732	0.106	0.0674	0.1326	0.0037	0.0238	0.2377	-0.0148	0.1711	7.5906	-2.737	-50.6317
8	2.2614	-0.2396	-1.7809	2.5826	-0.6528	5.416	0.1115	0.4732	0.2816	-0.4764	-0.109	0.2132	-0.4311	-0.4298	-0.0943	0.2817	0.0429	0.0284	0.2529	0.0326	0.2989	-8.0108	38.4834	-42.3444
9	0.7674	-0.7798	0.3605	2.9082	-0.3124	2.2203	-0.1556	-0.1017	0.0846	0.3397	-0.0214	0.1361	-0.3502	-0.018	-0.0525	0.3777	0.0357	0.0423	0.2038	0.0016	0.3038	-10.3339	48.4189	-29.8681
10	1.1598	-0.1354	-0.1801	2.8446	-0.1599	1.9579	0.0655	0.095	0.0604	-0.0538	-0.016	-0.1061	-0.175	0.0486	-0.0088	0.1622	0.0152	0.0347	0.1781	0.0269	0.2324	-2.5812	32.4517	-33.8518
11	1.0527	-0.5665	-0.0047	2.7009	-0.4518	2.0133	0.0223	0.0158	-0.0619	-0.0373	0.08	0.1763	-0.0983	-0.2023	-0.0416	0.1481	-0.0002	0.0146	0.1809	0.005	0.1872	-7.4817	24.2012	-26.1688
12	0.8058	0.1704	0.0186	0.8999	0.076	0.7033	0.0004	-0.0693	0.0103	0.1009	-0.0245	0.0803	0.0329	-0.0739	0.0045	0.0994	0.0148	0.0099	0.1838	0.0001	0.1212	-18.045	-7.1484	-21.9783
13	2.9113	-0.1767	-1.2092	1.8727	0.379	2.7346	-0.023	0.1779	-0.2257	-0.1783	0.0285	-0.1325	0.3369	0.2676	-0.0075	0.1828	0.0338	-0.0041	0.2415	-0.0101	0.1962	-14.1561	-22.7443	-35.9433
14	0.8497	0.2195	0.0124	1.5248	-0.3153	1.0681	-0.0106	0.1334	-0.0451	-0.0496	0.0469	0.1114	0.1101	-0.1138	-0.045	0.1041	0.0232	-0.0035	0.1986	-0.0258	0.152	-20.5435	-12.6419	-37.9586

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain A resi 1:49
2	X-RAY DIFFRACTION	2	chain A resi 50:103
3	X-RAY DIFFRACTION	3	chain A resi 104:195
4	X-RAY DIFFRACTION	4	chain A resi 196:237
5	X-RAY DIFFRACTION	5	chain A resi 238:379
6	X-RAY DIFFRACTION	6	chain A resi 380:412
7	X-RAY DIFFRACTION	7	chain A resi 413:491
8	X-RAY DIFFRACTION	8	chain B resi 1:49
9	X-RAY DIFFRACTION	9	chain B resi 50:103
10	X-RAY DIFFRACTION	10	chain B resi 104:195
11	X-RAY DIFFRACTION	11	chain B resi 196:237
12	X-RAY DIFFRACTION	12	chain B resi 238:379
13	X-RAY DIFFRACTION	13	chain B resi 380:412
14	X-RAY DIFFRACTION	14	chain B resi 413:491

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