PDB-4mwz: Crystal structure of N-methyl transferase from Plasmodium vivax c...

ID or keywords:

Entry

Database: PDB / ID: 4mwz

Title

Crystal structure of N-methyl transferase from Plasmodium vivax complexed with S-adenosyl methionine, phosphate and amodiaquine

Components

Phosphoethanolamine N-methyltransferase, putative

Keywords

transferase/transferase inhibitor / rossmann fold / transferase-transferase inhibitor complex

Function / homology

Function and homology information

phosphoethanolamine N-methyltransferase / S-adenosylmethionine-dependent methyltransferase activity
Similarity search - Function

Biological species

Plasmodium vivax (malaria parasite P. vivax)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 1.5 Å

Authors

Lukk, T. / Nair, S.K.

Citation

Journal: to be published
Title: Phosphoethanolamine N-methyl transferase is a Malarial drug target
Authors: Lukk, T. / Nair, S.K. / Mamoun, C.B.

History

Deposition	Sep 25, 2013	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 1, 2014	Provider: repository / Type: Initial release
Revision 1.1	Nov 12, 2014	Group: Structure summary
Revision 1.2	Sep 20, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif / struct_site Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _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	4mwz.cif.gz	244.5 KB	Display	PDBx/mmCIF format
PDB format	pdb4mwz.ent.gz	194.4 KB	Display	PDB format
PDBx/mmJSON format	4mwz.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4mwz_validation.pdf.gz	1.2 MB	Display	wwPDB validaton report
Full document	4mwz_full_validation.pdf.gz	1.2 MB	Display
Data in XML	4mwz_validation.xml.gz	28.7 KB	Display
Data in CIF	4mwz_validation.cif.gz	44.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/mw/4mwz ftp://data.pdbj.org/pub/pdb/validation_reports/mw/4mwz	HTTPS FTP

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Related structure data

Related structure data	4iv0C 3uj6S C: citing same article (ref.) S: Starting model for refinement
Similar structure data	1e3k-2 1e3k-1 4fgz-1 4oiu-d 1xq3-d 4apu-1 3bhi-d 4oil-d 4iv0-2 6nwl-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
Related items in Molecule of the Month	#234 - Jun 2019 MDM2 and Cancer similarity (1) #252 - Dec 2020 Hepatitis C Virus Protease/Helicase similarity (1) #9 - Sep 2000 Lysozyme similarity (1) #139 - Jul 2011 DNA Methyltransferase similarity (1)

Deposited unit

A: Phosphoethanolamine N-methyltransferase, putative

B: Phosphoethanolamine N-methyltransferase, putative

hetero molecules

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

1

A: Phosphoethanolamine N-methyltransferase, putative

hetero molecules

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

2

B: Phosphoethanolamine N-methyltransferase, putative

hetero molecules

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

Unit cell

Length a, b, c (Å)	37.440, 86.620, 78.270
Angle α, β, γ (deg.)	90.000, 103.230, 90.000
Int Tables number	4
Space group name H-M	P12₁1

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Protein , 1 types, 2 molecules AB

#1: Protein	Phosphoethanolamine N-methyltransferase, putative Mass: 31206.918 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Plasmodium vivax (malaria parasite P. vivax) Strain: Salvador I / Gene: PMT, PVX_083045 / Plasmid: pET24 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A5K867

#1: Protein

Phosphoethanolamine N-methyltransferase, putative

Mass: 31206.918 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Plasmodium vivax (malaria parasite P. vivax)
Strain: Salvador I / Gene: PMT, PVX_083045 / Plasmid: pET24 / Production host:

Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A5K867

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Non-polymers , 5 types, 734 molecules

#2: Chemical	ChemComp-SAM / S-ADENOSYLMETHIONINE Mass: 398.437 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₅H₂₂N₆O₅S
#3: Chemical	ChemComp-PO4 / PHOSPHATE ION Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO₄
#4: Chemical	ChemComp-BME / BETA-MERCAPTOETHANOL Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂H₆OS
#5: Chemical	ChemComp-CQA / 4-[(7-CHLOROQUINOLIN-4-YL)AMINO]-2-[(DIETHYLAMINO)METHYL]PHENOL / AMODIAQUINE / FLAVOQUINE Mass: 355.861 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂₀H₂₂ClN₃O / Comment: medication*YM
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 727 / 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: 1.98 Å³/Da / Density % sol: 37.86 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: Precipitant was 20% PEG 3350, 200 mM NH4-formate; protein solution contained 10 mM EDTA, 10 mM bME, 50 mM Tris-HCl, concentration was 15 mg/mL, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
Detector	Type: RAYONIX MX-225 / Detector: CCD / Date: Mar 23, 2012
Radiation	Monochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97872 Å / Relative weight: 1
Reflection	Number: 630541 / R_merge(I) obs: 0.097 / D res high: 1.5 Å / Num. obs: 152303 / % possible obs: 99.3
Diffraction reflection shell	Highest resolution: 1.5 Å / Lowest resolution: 1.54 Å / Num. obs: 11150 / % possible obs: 98.6 % / R_merge(I) obs: 0.56
Reflection	Resolution: 1.5→40 Å / Num. all: 153346 / Num. obs: 152303 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / R_sym value: 0.097 / Net I/σ(I): 9.76
Reflection shell	Resolution: 1.5→1.54 Å / Mean I/σ(I) obs: 2.36 / R_sym value: 0.56 / % possible all: 98.6

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Phasing

Phasing	Method: molecular replacement

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Processing

Software

Name	Version	Classification
PHASER		phasing
PHENIX	1.8.2_1309	refinement
PDB_EXTRACT	3.11	data extraction
HKL-2000		data collection
XDS		data reduction
XSCALE		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: pdb entry 3UJ6

3uj6

Resolution: 1.5→36.446 Å / Occupancy max: 1 / Occupancy min: 0.19 / FOM work R set: 0.9098 / SU ML: 0.13 / σ(F): 1.37 / Phase error: 16.34 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1779	3856	5 %	random
R_work	0.1517	-	-	-
all	0.1763	77124	-	-
obs	0.153	77118	99.31 %	-

Solvent computation

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

Displacement parameters

B_iso max: 74.99 Å² / B_iso mean: 16.1857 Å² / B_iso min: 3.23 Å²

Refinement step

Cycle: LAST / Resolution: 1.5→36.446 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4272	0	97	727	5096

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	4514
X-RAY DIFFRACTION	f_angle_d	1.137	6063
X-RAY DIFFRACTION	f_chiral_restr	0.075	635
X-RAY DIFFRACTION	f_plane_restr	0.004	749
X-RAY DIFFRACTION	f_dihedral_angle_d	15.822	1725

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 28

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
1.4999-1.5182	0.2521	134	0.2106	2547	2681	98
1.5182-1.5374	0.2443	136	0.1928	2565	2701	98
1.5374-1.5576	0.2179	137	0.1823	2604	2741	98
1.5576-1.5789	0.2266	135	0.1768	2570	2705	99
1.5789-1.6015	0.2229	137	0.1735	2609	2746	99
1.6015-1.6254	0.1794	138	0.1645	2624	2762	99
1.6254-1.6508	0.1897	134	0.1654	2535	2669	99
1.6508-1.6779	0.2045	136	0.1576	2597	2733	99
1.6779-1.7068	0.1954	139	0.1651	2631	2770	99
1.7068-1.7378	0.1928	136	0.162	2586	2722	99
1.7378-1.7713	0.2027	137	0.1553	2606	2743	99
1.7713-1.8074	0.1881	137	0.1556	2599	2736	99
1.8074-1.8467	0.1967	138	0.1602	2630	2768	99
1.8467-1.8897	0.1994	137	0.1554	2605	2742	99
1.8897-1.9369	0.1939	137	0.151	2600	2737	99
1.9369-1.9893	0.196	138	0.1477	2620	2758	100
1.9893-2.0478	0.1575	138	0.1496	2629	2767	100
2.0478-2.1139	0.163	139	0.1446	2637	2776	100
2.1139-2.1895	0.1733	139	0.1449	2644	2783	100
2.1895-2.2771	0.1878	137	0.1429	2591	2728	100
2.2771-2.3807	0.1823	140	0.1442	2663	2803	100
2.3807-2.5062	0.1815	138	0.1498	2632	2770	100
2.5062-2.6632	0.1832	140	0.1523	2645	2785	100
2.6632-2.8687	0.1622	139	0.1489	2647	2786	100
2.8687-3.1573	0.1781	139	0.1506	2642	2781	100
3.1573-3.6138	0.1522	139	0.1381	2633	2772	100
3.6138-4.5516	0.1418	140	0.1304	2670	2810	100
4.5516-36.4571	0.1639	142	0.1607	2701	2843	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	1.649	-0.2621	-0.7416	1.4672	0.2345	1.4253	-0.049	0.0614	0.0255	-0.0773	0.0311	0.0318	-0.0273	-0.005	0.0216	0.0533	-0.0133	-0.0039	0.0432	0.0164	0.0481	-5.0781	-14.94	-16.8347
2	0.9583	-0.0942	-0.5796	1.2349	-0.3081	1.3323	0.0666	-0.0918	0.16	0.0987	-0.0314	-0.0689	-0.2195	0.1683	-0.0204	0.0773	-0.023	-0.0111	0.068	-0.0112	0.0753	-2.4196	-10.4612	-6.8367
3	1.212	-0.1502	-0.661	0.8242	0.5089	1.784	-0.0668	-0.1256	-0.108	0.1783	0.0169	-0.0337	0.3252	0.1272	0.0198	0.1268	0.0193	0.003	0.063	0.0204	0.0698	-5.2469	-26.8935	-1.8163
4	4.0729	0.4013	-2.3955	1.4708	-0.2084	4.3244	-0.128	0.2656	-0.0938	-0.1296	-0.0233	-0.0951	0.089	0.0186	0.1071	0.1008	-0.0039	0.0062	0.0418	0.005	0.0779	0.6527	-30.6945	-25.5474
5	1.1882	-0.6718	-0.5895	1.5046	0.2678	1.6191	-0.1737	-0.0483	-0.1867	0.1257	0.0085	0.0479	0.3436	0.1651	0.1056	0.1197	0.0154	0.001	0.0629	0.0089	0.0639	-1.778	-31.2419	-12.885
6	4.0552	-0.7207	-3.2184	0.8797	1.0003	2.821	-0.4181	-0.7516	-0.1096	0.3495	0.3863	-0.3762	0.3563	0.67	0.0348	0.1882	0.0691	-0.0452	0.3158	-0.029	0.168	-2.0176	-20.0298	-38.2543
7	1.6792	0.0341	-0.1796	1.9674	0.9086	3.1879	0.0527	-0.0695	-0.0057	0.171	-0.0575	0.0578	0.0693	-0.127	-0.0165	0.0464	-0.0128	-0.0021	0.0425	-0.0044	0.056	-21.2763	-18.1714	-44.5378
8	1.2591	-0.2985	0.1663	1.2898	0.5092	1.32	-0.01	0.0223	-0.1651	0.0024	-0.0281	0.0976	0.0555	-0.085	0.0406	0.052	-0.0217	-0.0068	0.0517	-0.0134	0.0725	-16.8794	-29.897	-53.7079
9	1.3137	-0.9323	-1.0286	2.84	1.5061	3.601	-0.2062	-0.117	-0.1936	0.2615	-0.0234	0.1681	0.2292	-0.067	0.1918	0.1326	-0.0019	0.0178	0.0778	0.0298	0.0926	-16.8588	-33.3047	-41.914
10	1.4053	0.9267	0.8736	2.2705	1.9865	4.2406	-0.071	0.0039	-0.1895	0.0422	0.1122	-0.2484	0.1829	0.2893	-0.0196	0.071	0.0228	0.0016	0.0693	0.0032	0.1099	-2.6231	-32.7522	-52.3137
11	0.2609	-0.0532	0.0778	1.4033	0.6613	1.0889	-0.0294	-0.0695	0.0208	0.0012	0.0853	-0.1624	0.0121	0.1281	-0.0403	0.037	0.0001	-0.0154	0.0651	-0.0148	0.0806	-2.8045	-22.4557	-53.2798
12	1.2026	0.0422	0.0787	2.0012	0.4585	1.3527	-0.0098	-0.1472	0.249	-0.1648	0.19	-0.4007	-0.3459	0.2103	-0.0794	0.0604	-0.0335	-0.004	0.1018	-0.0637	0.1479	-5.3154	-10.3879	-49.4625
13	1.9638	-1.8069	-1.9328	2.7182	1.707	2.2932	0.101	0.0563	0.1924	-0.1921	-0.0061	-0.1793	-0.2332	0.0883	-0.084	0.0958	-0.0058	0.0294	0.0705	0.0067	0.0716	-3.7835	-15.5155	-62.6056
14	3.3745	0.2942	-1.6441	1.4583	-0.1385	2.3491	0.1006	0.0212	0.2157	-0.0999	-0.086	0.2301	-0.0927	-0.2828	-0.0312	0.0599	0.0082	-0.0225	0.0682	-0.0226	0.0881	-23.8594	-6.7826	-48.2065
15	1.5904	-0.4356	-0.0442	1.0436	0.5308	1.6258	0.0885	-0.4429	-0.09	0.3748	-0.1698	-0.001	-0.0539	-0.0095	0.003	0.1324	-0.0372	0.0195	0.1317	-0.0229	0.0985	-21.5441	-6.5289	-36.8057
16	1.4593	-0.7853	-0.5886	2.1395	0.4732	0.9183	0.1221	0.0656	0.1052	-0.2585	-0.0544	-0.1659	-0.2078	-0.0688	-0.0498	0.0581	-0.0054	0.0133	0.0426	0.0068	0.0489	-9.527	-12.3892	-57.9186

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 14 through 84 )	A
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 85 through 145 )	A
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 146 through 203 )	A
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 204 through 230 )	A
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 231 through 263 )	A
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 0 through 17 )	B
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 18 through 44 )	B
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 45 through 84 )	B
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 85 through 105 )	B
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 106 through 119 )	B
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 120 through 145 )	B
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 146 through 182 )	B
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 183 through 203 )	B
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 204 through 220 )	B
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 221 through 249 )	B
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 250 through 263 )	B

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