PDB-5wp4: Arabidopsis thaliana phosphoethanolamine N-methyltransferase 1 (A...

ID or keywords:

Entry

Database: PDB / ID: 5wp4

Title

Arabidopsis thaliana phosphoethanolamine N-methyltransferase 1 (AtPMT1, XIOPTL) in complex with SAH and phosphocholine

Components

Phosphoethanolamine N-methyltransferase 1

Keywords

TRANSFERASE / Phosphoethanolamine N-Methyltransferase / AtPMT1 / XIOPTL

Function / homology

Function and homology information

choline biosynthetic process / pollen tube guidance / post-embryonic root development / phosphoethanolamine N-methyltransferase activity / pollen tube growth / phosphoethanolamine N-methyltransferase / unidimensional cell growth / pollen development / phosphatidylcholine biosynthetic process / methyltransferase activity ...
Similarity search - Function

Biological species

Arabidopsis thaliana (thale cress)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.341 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)	AI097119	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	Nov 27, 2019	Group: Author supporting evidence / Category: pdbx_audit_support Item: _pdbx_audit_support.funding_organization / _pdbx_audit_support.grant_number
Revision 1.3	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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PDBx/mmCIF format	5wp4.cif.gz	233.4 KB	Display	PDBx/mmCIF format
PDB format	pdb5wp4.ent.gz	184.2 KB	Display	PDB format
PDBx/mmJSON format	5wp4.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	5wp4_validation.pdf.gz	958.2 KB	Display	wwPDB validaton report
Full document	5wp4_full_validation.pdf.gz	961.2 KB	Display
Data in XML	5wp4_validation.xml.gz	26 KB	Display
Data in CIF	5wp4_validation.cif.gz	40.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/wp/5wp4 ftp://data.pdbj.org/pub/pdb/validation_reports/wp/5wp4	HTTPS FTP

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Related structure data

Related structure data	5wp5C 4krgS 4krhS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	1qds-1 2v5l-1 1amp-1 3db1-2 1l5o-1 1amk-1 1iig-d 5dro-d 3s04-d 3wyn-d 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 1

hetero molecules

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

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	49.261, 86.032, 68.242
Angle α, β, γ (deg.)	90.00, 106.15, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Phosphoethanolamine N-methyltransferase 1 / PEAMT 1 / Protein XIPOTL 1 Mass: 56175.512 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: NMT1, PEAMT, XPL1, At3g18000, MEB5.22 / Production host: Escherichia coli (E. coli) References: UniProt: Q9FR44, phosphoethanolamine N-methyltransferase
#2: 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
#3: Chemical	ChemComp-PC / PHOSPHOCHOLINE Mass: 184.151 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₅H₁₅NO₄P
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 650 / 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: 2.47 Å³/Da / Density % sol: 50.25 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, hanging drop Details: 16% w/v PEG8000, 0.04 M potassium phosphate monobasic, 20% v/v glycerol

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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: Nov 29, 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: 1.34→26.734 Å / Num. obs: 121932 / % possible obs: 99 % / Redundancy: 3.7 % / Net I/σ(I): 30.2
Reflection shell	Highest resolution: 1.34 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: 1.341→26.734 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 15.44

	R_factor	Num. reflection	% reflection
R_free	0.1661	6098	5.02 %
R_work	0.1517	-	-
obs	0.1524	121515	99.53 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.341→26.734 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3901	0	74	650	4625

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	4196
X-RAY DIFFRACTION	f_angle_d	1.106	5674
X-RAY DIFFRACTION	f_dihedral_angle_d	18.034	1635
X-RAY DIFFRACTION	f_chiral_restr	0.074	591
X-RAY DIFFRACTION	f_plane_restr	0.005	735

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 (%)
1.3407-1.356	0.2362	213	0.2302	3661	X-RAY DIFFRACTION	95
1.356-1.3719	0.2303	217	0.2192	3827	X-RAY DIFFRACTION	100
1.3719-1.3887	0.2138	205	0.2229	3857	X-RAY DIFFRACTION	100
1.3887-1.4062	0.238	189	0.2097	3841	X-RAY DIFFRACTION	100
1.4062-1.4247	0.2198	229	0.2024	3813	X-RAY DIFFRACTION	100
1.4247-1.4443	0.2066	194	0.195	3879	X-RAY DIFFRACTION	100
1.4443-1.4649	0.2127	180	0.1817	3831	X-RAY DIFFRACTION	100
1.4649-1.4868	0.2045	212	0.1744	3884	X-RAY DIFFRACTION	100
1.4868-1.51	0.1748	185	0.1651	3873	X-RAY DIFFRACTION	100
1.51-1.5347	0.1762	201	0.1579	3843	X-RAY DIFFRACTION	100
1.5347-1.5612	0.1604	202	0.1553	3864	X-RAY DIFFRACTION	100
1.5612-1.5896	0.1597	206	0.1546	3852	X-RAY DIFFRACTION	100
1.5896-1.6202	0.1578	207	0.1457	3864	X-RAY DIFFRACTION	100
1.6202-1.6532	0.1498	226	0.1482	3832	X-RAY DIFFRACTION	100
1.6532-1.6892	0.192	201	0.1507	3870	X-RAY DIFFRACTION	100
1.6892-1.7285	0.1681	199	0.146	3844	X-RAY DIFFRACTION	100
1.7285-1.7717	0.1714	195	0.1443	3867	X-RAY DIFFRACTION	100
1.7717-1.8196	0.1836	186	0.1456	3878	X-RAY DIFFRACTION	100
1.8196-1.8731	0.1492	212	0.1427	3844	X-RAY DIFFRACTION	100
1.8731-1.9335	0.1635	225	0.1435	3842	X-RAY DIFFRACTION	100
1.9335-2.0026	0.165	183	0.1427	3902	X-RAY DIFFRACTION	100
2.0026-2.0828	0.1521	232	0.1458	3824	X-RAY DIFFRACTION	100
2.0828-2.1775	0.1446	215	0.1392	3845	X-RAY DIFFRACTION	100
2.1775-2.2923	0.1638	185	0.1403	3909	X-RAY DIFFRACTION	100
2.2923-2.4358	0.1578	215	0.142	3866	X-RAY DIFFRACTION	100
2.4358-2.6237	0.1552	222	0.1508	3868	X-RAY DIFFRACTION	100
2.6237-2.8875	0.1647	201	0.1503	3875	X-RAY DIFFRACTION	100
2.8875-3.3046	0.1561	173	0.1497	3922	X-RAY DIFFRACTION	100
3.3046-4.161	0.1514	203	0.1358	3850	X-RAY DIFFRACTION	99
4.161-26.7394	0.1836	185	0.1644	3690	X-RAY DIFFRACTION	93

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	3.0289	-0.3486	-0.394	0.9312	-0.5787	2.7356	-0.0483	-0.0042	-0.0258	0.1992	-0.0491	-0.0484	-0.0444	0.1242	0.1134	0.291	0.0312	-0.0067	0.1908	0.0474	0.1493	15.4814	-2.8615	39.5641
2	4.4594	-0.5286	0.0897	1.8228	1.4183	1.1665	-0.2235	-0.549	0.8369	0.5711	0.0098	0.0487	-0.7183	-0.5833	-0.0834	0.6223	0.1246	0.035	0.315	-0.044	0.2789	6.1651	12.2435	42.7373
3	1.3033	-0.2329	-0.0128	2.0332	0.1522	2.1192	-0.0416	-0.1211	0.0337	0.1855	0.009	0.3271	-0.1922	-0.5683	0.0648	0.1857	0.0469	0.0202	0.2318	0.0065	0.1904	-1.1011	4.1583	29.118
4	3.8717	-0.2584	0.1323	1.8991	-0.4886	2.6914	-0.1044	-0.1127	-0.2311	0.1899	0.0776	0.3361	0.2045	-0.6706	-0.0816	0.2297	-0.0501	0.0541	0.2652	0.0317	0.1936	-1.8021	-6.1412	33.5405
5	1.2965	-0.1229	0.2422	0.8692	-0.2501	2.8592	-0.0892	0.0486	-0.1231	0.0415	0.0072	0.056	0.0513	-0.0392	0.0608	0.1586	-0.0163	-0.005	0.1237	0.0208	0.157	9.9115	-1.3787	22.2936
6	1.9423	-0.5274	-0.1478	0.3151	0.5911	1.914	-0.2096	-0.3054	0.1332	0.4395	0.0005	-0.1804	-0.5988	0.5546	-0.9218	0.3497	-0.0732	-0.0978	0.2071	0.0491	0.1584	20.6751	7.693	33.5753
7	3.8539	0.5228	0.0199	2.8642	0.7416	3.6332	0.063	0.155	-0.1537	-0.0771	0.0266	-0.3722	-0.0517	-0.2467	0.1222	0.1848	-0.0418	-0.0314	0.1256	0.0223	0.1729	15.3116	5.5052	13.0579
8	1.2714	0.0016	0.0214	2.3379	1.487	4.0549	-0.1067	-0.1432	0.0748	0.1988	-0.0065	0.1632	-0.5657	0.0176	-0.0361	0.2941	0.0205	-0.0333	0.1615	0.0111	0.1891	8.3008	9.9322	19.2503
9	1.5867	0.2599	-0.1057	2.8077	0.463	1.5831	-0.0484	-0.0749	0.0047	0.0548	0.0134	-0.0595	-0.4469	-0.0782	0.0841	0.1791	-0.0006	-0.0324	0.089	0.0279	0.1066	9.0865	10.596	20.2767
10	1.5785	0.8444	-0.5192	1.8579	0.044	1.4369	0.0878	-0.0639	-0.2083	0.0583	-0.1012	-0.1826	0.1763	0.0214	-0.0109	0.1472	0.0012	-0.0466	0.1066	0.0249	0.146	25.3581	17.531	7.7349
11	2.5832	0.2669	-0.9937	2.0449	-0.5636	2.5021	0.0745	0.0586	0.4634	0.0992	-0.0484	-0.1206	-0.1661	0.0655	-0.0768	0.1154	-0.0056	0.013	0.0558	-0.015	0.1124	16.2393	39.2767	7.7848
12	0.6733	-0.1039	0.1719	2.0426	-0.2486	0.5247	0.08	-0.1329	-0.0239	0.2397	-0.0628	0.0328	0.034	-0.0855	-0.02	0.1568	-0.0349	-0.0082	0.1373	0.0036	0.1245	13.2233	24.1001	12.0794
13	1.8002	0.3069	0.1798	0.8481	0.0677	1.2036	0.0083	0.2706	0.0187	-0.0951	0.0295	-0.0155	0.0166	0.0015	-0.0326	0.107	0.0026	-0.0225	0.1278	0.0058	0.1066	18.0098	26.6356	-6.0818
14	1.5374	0.7408	-0.1196	2.0044	-0.4482	1.4027	0.0795	-0.3283	0.0318	0.3127	-0.1521	-0.2162	-0.1724	0.1182	0.0412	0.1217	-0.0231	-0.025	0.1696	0.0273	0.1408	33.3676	33.4351	5.4451
15	2.6943	0.6034	-0.3189	1.098	-0.0777	1.4749	0.0641	-0.0636	-0.3837	0.1101	-0.1177	-0.2133	0.0977	0.2723	-0.063	0.1017	0.003	-0.0323	0.1172	0.0426	0.1556	33.6357	26.9168	1.975

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain A resi 6:29
2	X-RAY DIFFRACTION	2	chain A resi 30:41
3	X-RAY DIFFRACTION	3	chain A resi 42:69
4	X-RAY DIFFRACTION	4	chain A resi 70:104
5	X-RAY DIFFRACTION	5	chain A resi 105:161
6	X-RAY DIFFRACTION	6	chain A resi 162:182
7	X-RAY DIFFRACTION	7	chain A resi 183:190
8	X-RAY DIFFRACTION	8	chain A resi 191:218
9	X-RAY DIFFRACTION	9	chain A resi 219:231
10	X-RAY DIFFRACTION	10	chain A resi 232:267
11	X-RAY DIFFRACTION	11	chain A resi 268:282
12	X-RAY DIFFRACTION	12	chain A resi 283:342
13	X-RAY DIFFRACTION	13	chain A resi 343:423
14	X-RAY DIFFRACTION	14	chain A resi 424:453
15	X-RAY DIFFRACTION	15	chain A resi 454:491

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