PDB-4iv0: Crystal structure of N-methyl transferase from Plasmodium vivax c...

ID or keywords:

Entry

Database: PDB / ID: 4iv0

Title

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

Components

Phosphoethanolamine N-methyltransferase, putative

Keywords

TRANSFERASE / AdoMet_MTase

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: 1.4 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.

History

Deposition	Jan 22, 2013	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Feb 19, 2014	Provider: repository / Type: Initial release
Revision 1.1	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_conn / 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_conn.pdbx_leaving_atom_flag / _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	4iv0.cif.gz	239.7 KB	Display	PDBx/mmCIF format
PDB format	pdb4iv0.ent.gz	188.5 KB	Display	PDB format
PDBx/mmJSON format	4iv0.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4iv0_validation.pdf.gz	977.5 KB	Display	wwPDB validaton report
Full document	4iv0_full_validation.pdf.gz	978.8 KB	Display
Data in XML	4iv0_validation.xml.gz	30.7 KB	Display
Data in CIF	4iv0_validation.cif.gz	49.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/iv/4iv0 ftp://data.pdbj.org/pub/pdb/validation_reports/iv/4iv0	HTTPS FTP

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Related structure data

Related structure data	4mwzC 3uj6S 4iv8 S: Starting model for refinement C: citing same article (ref.)
Similar structure data	1k07-2 5mwp-d 3blm-d 5wck-2 3pb6-d 3qsd-d 4wvd-2 3v91-d 4r6w-2 3dct-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

67.3 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
33.6 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
33.7 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	38.170, 86.870, 79.580
Angle α, β, γ (deg.)	90.000, 101.050, 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: 33096.000 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Plasmodium vivax (malaria parasite P. vivax) Strain: Sal-1 / Gene: PVX_083045 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: A5K867, phosphoethanolamine N-methyltransferase

#1: Protein

Phosphoethanolamine N-methyltransferase, putative

Mass: 33096.000 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Plasmodium vivax (malaria parasite P. vivax)
Strain: Sal-1 / Gene: PVX_083045 / Plasmid: pET28 / Production host:

Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: A5K867, phosphoethanolamine N-methyltransferase

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Non-polymers , 5 types, 998 molecules

#2: Chemical	ChemComp-PO4 / PHOSPHATE ION Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO₄
#3: Chemical	ChemComp-SAM / S-ADENOSYLMETHIONINE Mass: 398.437 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₅H₂₂N₆O₅S
#4: Chemical	ChemComp-BME / BETA-MERCAPTOETHANOL Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₆OS
#5: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₆O₂
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 992 / 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: 1.96 Å³/Da / Density % sol: 37.13 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: Protein solution was at 15 mg/mL containing 20 mM Tris (pH 7.5), 100 mM NaCl, 10 mM EDTA and 10 mM bME, 5 mM SAM. Mother liqueur contained 0.2 M Ammonium formate and 20% PEG 3,350. ...Details: Protein solution was at 15 mg/mL containing 20 mM Tris (pH 7.5), 100 mM NaCl, 10 mM EDTA and 10 mM bME, 5 mM SAM. Mother liqueur contained 0.2 M Ammonium formate and 20% PEG 3,350. Cryoprotectant was 30% PEG 3,350 , VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal

Density Matthews: 1.96 Å³/Da / Density % sol: 37.13 %

Crystal grow

Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Protein solution was at 15 mg/mL containing 20 mM Tris (pH 7.5), 100 mM NaCl, 10 mM EDTA and 10 mM bME, 5 mM SAM. Mother liqueur contained 0.2 M Ammonium formate and 20% PEG 3,350. ...

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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 14, 2011

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

Resolution: 1.4→20 Å / Num. all: 100044 / Num. obs: 98848 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / B_iso Wilson estimate: 17.259 Å² / R_merge(I) obs: 0.082 / Net I/σ(I): 13.61

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Highest resolution (Å)	R_merge(I) obs	Mean I/σ(I) obs	Num. measured obs	Num. unique obs	% possible all
1.4-1.44		0.556	2.99	41913	7155	97.4
1.44-1.48		0.444	3.84	41774	7038	97.2
1.48-1.52		0.372	4.55	41175	6857	98.4
1.52-1.57		0.31	5.52	40794	6690	98.5
1.57-1.62		0.264	6.47	39649	6430	98.2
1.62-1.67		0.227	7.46	39250	6299	98.4
1.67-1.74		0.196	8.69	38238	6110	98.7
1.74-1.81		0.164	10.34	37045	5882	99.5
1.81-1.89		0.136	12.23	35579	5621	99.2
1.89-1.98		0.112	14.52	34134	5396	99.3
1.98-2.09		0.09	18.02	32237	5109	99.5
2.09-2.21		0.08	19.46	30948	4902	99.5
2.21-2.37		0.073	21.05	28791	4570	99.7
2.37-2.56		0.066	23.65	26951	4292	99.5
2.56-2.8		0.06	25.68	24535	3912	99.8
2.8-3.13		0.053	28.37	22329	3580	99.9
3.13-3.61		0.046	30.84	19637	3141	99.6
3.61-4.43		0.042	32.98	16649	2664	99.7
4.43-6.26		0.041	33.53	13012	2084	99.8
	6.26	0.038	33.26	6717	1116	96

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Phasing

Phasing	Method: molecular replacement

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Processing

Software

Name	Version	Classification
XSCALE		data scaling
PHASER		phasing
PHENIX	1.7.3_928	refinement
PDB_EXTRACT	3.11	data extraction
HKL-2000		data collection
XDS		data reduction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3UJ6

3uj6

Resolution: 1.4→19.684 Å / Occupancy max: 1 / Occupancy min: 0.17 / FOM work R set: 0.9157 / SU ML: 0.14 / σ(F): 2.03 / Phase error: 15.91 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1785	4943	5 %	random
R_work	0.1573	-	-	-
all	0.166	100044	-	-
obs	0.1583	98845	98.87 %	-

Solvent computation

Shrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 32.677 Å² / k_sol: 0.308 e/Å³

Displacement parameters

B_iso max: 70.3 Å² / B_iso mean: 14.4367 Å² / B_iso min: 3.08 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.0568 Å²	0 Å²	0.0505 Å²
2-	-	0.0158 Å²	-0 Å²
3-	-	-	0.041 Å²

Refinement step

Cycle: LAST / Resolution: 1.4→19.684 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4309	0	72	992	5373

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	4556
X-RAY DIFFRACTION	f_angle_d	1.137	6125
X-RAY DIFFRACTION	f_chiral_restr	0.078	646
X-RAY DIFFRACTION	f_plane_restr	0.005	759
X-RAY DIFFRACTION	f_dihedral_angle_d	13.224	1760

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
1.4-1.4159	0.2287	161	0.2105	3059	3220	96
1.4159-1.4326	0.2196	161	0.2027	3056	3217	99
1.4326-1.4501	0.2317	163	0.1941	3087	3250	98
1.4501-1.4684	0.2112	162	0.1819	3086	3248	96
1.4684-1.4877	0.2278	161	0.1849	3066	3227	99
1.4877-1.5081	0.234	165	0.179	3130	3295	99
1.5081-1.5296	0.194	164	0.1695	3109	3273	97
1.5296-1.5524	0.2452	161	0.1638	3067	3228	99
1.5524-1.5767	0.1988	164	0.1624	3120	3284	99
1.5767-1.6025	0.1799	163	0.1558	3096	3259	98
1.6025-1.6302	0.1767	165	0.1554	3134	3299	99
1.6302-1.6598	0.1954	164	0.1561	3103	3267	98
1.6598-1.6917	0.1935	164	0.1532	3119	3283	100
1.6917-1.7262	0.1813	166	0.1489	3159	3325	99
1.7262-1.7637	0.1806	162	0.1546	3071	3233	99
1.7637-1.8047	0.1763	166	0.1548	3162	3328	99
1.8047-1.8498	0.1976	164	0.1536	3115	3279	99
1.8498-1.8998	0.1765	166	0.1571	3161	3327	99
1.8998-1.9556	0.1868	163	0.165	3095	3258	99
1.9556-2.0187	0.1867	168	0.1577	3190	3358	99
2.0187-2.0908	0.1843	165	0.1563	3128	3293	100
2.0908-2.1744	0.161	166	0.1497	3153	3319	100
2.1744-2.2732	0.1689	167	0.1592	3175	3342	100
2.2732-2.3929	0.1658	167	0.1475	3174	3341	100
2.3929-2.5425	0.1763	166	0.158	3153	3319	100
2.5425-2.7383	0.1765	167	0.1624	3175	3342	100
2.7383-3.013	0.1878	166	0.1592	3159	3325	100
3.013-3.447	0.1665	167	0.148	3174	3341	100
3.447-4.3352	0.1421	168	0.1367	3195	3363	100
4.3352-19.6858	0.1587	171	0.1569	3231	3402	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	0.0003	-0.0004	0.0003	-0.0003	-0.0002	0.0004	-0.0007	-0.0015	-0.0016	0.0042	0.0049	-0.0082	-0.0009	-0.0022	0	0.0397	0.0282	-0.0337	0.075	0.0198	0.0378	6.1103	-20.2593	0.5209
2	0.0005	-0.0022	0	0.0015	0.002	0.0009	0.0058	0.0031	-0.0528	0.0061	0.03	0.0222	0.0122	-0.0088	-0	0.0044	0.006	-0.0152	0.0003	0.0283	-0.0392	-9.4105	-27.0889	-11.9026
3	-0.0004	0.0003	0.0002	0.0004	-0.0002	0.0004	-0.0031	-0.0005	-0.0068	0.0046	-0.0037	0.0044	0.0051	-0.0012	-0	0.063	0.0059	0.0092	0.0353	0.021	0.0517	-7.0461	-35.0881	-4.5326
4	0.0002	-0.0006	0.0009	0.0003	0.0004	0.0003	-0.0072	-0.0044	-0.0022	-0.0012	-0.001	-0.0048	0.0031	0.0043	-0	0.0079	0.0384	-0.0153	0.0018	-0.0186	0.0301	6.5548	-34.3216	-15.1159
5	-0.0002	-0.0011	-0.0005	-0.0002	0.0016	-0.0011	-0.0077	0.0016	0.0005	0.0019	0.0034	-0.0137	-0.0008	0.0115	0	-0.1272	0.0697	0.0096	-0.0259	-0.0247	-0.0114	6.2313	-24.0758	-16.2209
6	0.001	0.0001	0.0005	0.0003	-0.0012	0.0008	-0.0358	0.005	0.0175	-0.0025	-0.0174	-0.0292	-0.0001	0.0123	-0	-0.0654	0.0104	-0.0401	-0.0361	-0.0168	-0.0156	3.7123	-11.8578	-12.5413
7	0	-0.0008	-0.0013	-0.0004	-0.0005	0.0004	0.0031	-0.0013	0.0068	-0.001	0.0051	0.0039	-0.0098	0.0044	-0	-0.0325	-0.0013	0.055	0.0182	-0.0128	-0.0356	4.4689	-16.9737	-25.4414
8	0.0002	-0.0011	-0.0019	-0.0014	0.0003	-0.0005	0.0183	-0.0309	0.0064	0.0127	-0.0014	0.0024	-0.0068	-0.0218	-0	-0.1045	0.0894	0.0436	-0.0528	0.0222	-0.1179	-12.9661	-8.3406	-3.2936
9	0.0008	0.0006	-0.0006	0.0007	-0.0004	0.0006	-0.0051	0.0108	0.0019	-0.0033	-0.0011	-0.0031	-0.0039	0.0012	-0	-0.0098	0.0171	0.0189	-0.0222	-0.0162	0.0042	-0.3954	-15.9206	-21.8279
10	0	0.0001	0.0005	0.0003	0.001	0.0003	0.0112	-0.0077	-0.0029	0.0071	0.0063	-0.0109	0.0018	0.0115	0	0.0187	-0.0151	0.0198	0.0057	-0.0077	0.0304	-0.219	-27.1272	-56.0471
11	0.0009	-0.0001	-0.0023	0.0021	0.0009	0.0027	0.0024	0.0102	0.0136	-0.011	0.0212	0.0202	-0.0054	0.0032	-0	0.0568	-0.0011	-0.0032	0.0604	0.0011	0.0631	-21.0327	-14.377	-55.0763
12	0.0001	0	-0.0005	0.0008	-0.0009	0	0.0069	0.0016	0.0098	-0.0044	0.0073	0.006	-0.0093	-0.0005	-0	0.031	-0.0073	-0.0005	-0.0223	0.017	0.0022	-10.7224	-7.8113	-57.5327
13	0.0011	0.0009	-0.0003	0.0012	-0.001	0.0007	0.0084	-0.0067	0.0102	0.0076	0.0017	0.0068	-0.0075	0.0052	-0	0.0469	-0.0011	-0.0038	0.05	-0.0013	0.0472	-16.1096	-14.5591	-40.3006
14	0.0026	0.0036	-0.0019	0.0016	-0.0001	-0.0001	0.0059	-0.0157	0.0033	0.0091	-0.0074	0.0069	0.0125	0.0022	0	0.0559	0.0012	-0.001	0.0374	0.0022	0.0545	-18.3519	-27.3639	-42.0446
15	0.0008	0.0019	-0.0016	0.0027	-0.002	0.0023	-0.0003	-0.0196	-0.0019	0.0058	-0.0253	-0.0146	0.0155	0.0061	-0	0.057	-0.0004	-0.0024	0.0622	0.0026	0.062	-16.273	-28.8828	-40.5793
16	0.0007	0.0002	0.001	0	0.0011	0.0015	-0.0034	0.0117	0.0012	-0.0171	0.0024	0.0015	-0.0028	0.0089	0	0.0741	-0.0053	0.0042	0.0661	-0.0004	0.0428	-13.0866	-32.9278	-64.8471
17	0.0003	-0.0006	0.0003	0.0004	0.0008	0.0013	-0.0047	0.0076	0.0003	0.0018	0.0031	-0.0067	-0.0067	0.013	-0	0.0809	-0.0024	0.0053	0.0629	0.0004	0.0484	-6.5021	-35.4043	-59.1499
18	0.0011	0.0011	-0.0004	0.001	-0.0012	0.0015	0.0081	-0.0115	0.0015	0.0062	-0.004	0.0079	0.0043	-0.0028	-0	0.0637	0.0027	-0.002	0.0324	-0.0009	0.0634	-23.1142	-26.9911	-43.5662

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resseq 2:17)	A	2 - 17
2	X-RAY DIFFRACTION	2	chain 'A' and (resseq 18:84)	A	18 - 84
3	X-RAY DIFFRACTION	3	chain 'A' and (resseq 85:105)	A	85 - 105
4	X-RAY DIFFRACTION	4	chain 'A' and (resseq 106:119)	A	106 - 119
5	X-RAY DIFFRACTION	5	chain 'A' and (resseq 120:145)	A	120 - 145
6	X-RAY DIFFRACTION	6	chain 'A' and (resseq 146:182)	A	146 - 182
7	X-RAY DIFFRACTION	7	chain 'A' and (resseq 183:203)	A	183 - 203
8	X-RAY DIFFRACTION	8	chain 'A' and (resseq 204:249)	A	204 - 249
9	X-RAY DIFFRACTION	9	chain 'A' and (resseq 250:264)	A	250 - 264
10	X-RAY DIFFRACTION	10	chain 'B' and (resseq 5:28)	B	5 - 28
11	X-RAY DIFFRACTION	11	chain 'B' and (resseq 29:84)	B	29 - 84
12	X-RAY DIFFRACTION	12	chain 'B' and (resseq 85:105)	B	85 - 105
13	X-RAY DIFFRACTION	13	chain 'B' and (resseq 106:145)	B	106 - 145
14	X-RAY DIFFRACTION	14	chain 'B' and (resseq 146:166)	B	146 - 166
15	X-RAY DIFFRACTION	15	chain 'B' and (resseq 167:203)	B	167 - 203
16	X-RAY DIFFRACTION	16	chain 'B' and (resseq 204:228)	B	204 - 228
17	X-RAY DIFFRACTION	17	chain 'B' and (resseq 229:249)	B	229 - 249
18	X-RAY DIFFRACTION	18	chain 'B' and (resseq 250:264)	B	250 - 264

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Protein , 1 types, 2 molecules AB

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Non-polymers , 5 types, 998 molecules

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Movie

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Structure viewers

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Open data

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Validation report

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Assembly

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Components

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Protein , 1 types, 2 molecules AB

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Non-polymers , 5 types, 998 molecules

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Experimental details

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Experiment

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Sample preparation

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Data collection

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Phasing

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Processing

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Yorodumi