PDB-4krh: SeMet Haemonchus contortus Phosphoethanolamine N-methyltransferas...

ID or keywords:

Entry

Database: PDB / ID: 4krh

Title

SeMet Haemonchus contortus Phosphoethanolamine N-methyltransferase 2 in complex with S-adenosyl-L-methionine

Components

Phosphoethanolamine N-methyltransferase 2

Keywords

TRANSFERASE /

methyltransferase

Function / homology

Phosphoethanolamine N-methyltransferase 2, N-terminal / Phosphoethanolamine N-methyltransferase 2 N-terminal /

phosphoethanolamine N-methyltransferase / Methyltransferase type 11 /

Methyltransferase domain / S-adenosylmethionine-dependent methyltransferase activity / S-adenosyl-L-methionine-dependent methyltransferase superfamily /

S-ADENOSYLMETHIONINE /

phosphoethanolamine N-methyltransferase

Function and homology information

Biological species

Haemonchus contortus (barber pole worm)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 3 Å

Authors

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

Citation

Journal: Structure / Year: 2013
Title: Evolution of structure and mechanistic divergence in di-domain methyltransferases from nematode phosphocholine biosynthesis.
Authors: Lee, S.G. / Jez, J.M.

History

Deposition	May 16, 2013	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Sep 25, 2013	Provider: repository / Type: Initial release
Revision 1.1	Oct 30, 2013	Group: Database references

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4krh.cif.gz	359 KB	Display	PDBx/mmCIF format
PDB format	pdb4krh.ent.gz	311.2 KB	Display	PDB format
PDBx/mmJSON format	4krh.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/kr/4krh ftp://data.pdbj.org/pub/pdb/validation_reports/kr/4krh	HTTPS FTP

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Related structure data

Related structure data	4krgC 4kriC C: citing same article (ref.)
Similar structure data	6uwy-4 4yqx-2 2xyq-d 6kvz-d 1x1b-d 6d9e-d 6t6a-1 6ktx-d 6i7h-d 6yf8-1 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	#139 - Jul 2011 DNA Methyltransferase similarity (1)

Deposited unit

A: Phosphoethanolamine N-methyltransferase 2

B: Phosphoethanolamine N-methyltransferase 2

hetero molecules

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

1

A: Phosphoethanolamine N-methyltransferase 2

hetero molecules

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

2

B: Phosphoethanolamine N-methyltransferase 2

hetero molecules

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

Unit cell

Length a, b, c (Å)	184.542, 184.542, 184.542
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	197
Space group name H-M	I23

Components on special symmetry positions

ID	Model	Components
1	1	B-338- GLU

#1: Protein	Phosphoethanolamine N-methyltransferase 2 / Mass: 50046.145 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Haemonchus contortus (barber pole worm) Plasmid: pET-28a-HcPMT2 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta II (DE3) / References: UniProt: U5HK48*PLUS
#2: Chemical	ChemComp-SAM / S-ADENOSYLMETHIONINE / S-Adenosyl methionine Mass: 398.437 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₅H₂₂N₆O₅S

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.62 Å³/Da / Density % sol: 52.99 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 9 Details: 0.1 M Tris-HCl, 25% PEG-400, pH 9.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.979 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 20, 2010 Details: Rosenbaum-Rock high-resolution double-crystal monochromator
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.979 Å / Relative weight: 1
Reflection	Resolution: 3→41.3 Å / Num. obs: 21008 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0

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Processing

Software

Name	Version	Classification
HKL-3000		data collection
SHELXS		phasing
PHENIX	(phenix.refine: 1.8.1_1168)	refinement
HKL-3000		data reduction
HKL-3000		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 3→41.265 Å / SU ML: 0.4 / σ(F): 1.34 / Phase error: 29.42 / Stereochemistry target values: MLHL

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2862	1079	5.14 %	random
R_work	0.2392	-	-	-
obs	0.2415	21008	99.59 %	-
all	-	21029	-	-

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 3→41.265 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6932	0	54	0	6986

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	7134
X-RAY DIFFRACTION	f_angle_d	1.011	9618
X-RAY DIFFRACTION	f_dihedral_angle_d	16.293	2693
X-RAY DIFFRACTION	f_chiral_restr	0.075	1038
X-RAY DIFFRACTION	f_plane_restr	0.005	1243

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 (%)
3-3.1356	0.3465	135	0.3027	2485	X-RAY DIFFRACTION	99
3.1356-3.3009	0.3137	125	0.2942	2468	X-RAY DIFFRACTION	100
3.3009-3.5076	0.3089	137	0.2799	2442	X-RAY DIFFRACTION	100
3.5076-3.7783	0.2849	144	0.2547	2477	X-RAY DIFFRACTION	100
3.7783-4.1582	0.2807	140	0.2355	2480	X-RAY DIFFRACTION	100
4.1582-4.7591	0.254	112	0.2165	2511	X-RAY DIFFRACTION	100
4.7591-5.993	0.2693	139	0.2412	2518	X-RAY DIFFRACTION	100
5.993-41.2687	0.2954	147	0.2175	2548	X-RAY DIFFRACTION	99

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	3.099	2.1004	-0.7462	5.5297	3.3174	3.8851	-0.2165	0.824	0.2328	-1.2912	-0.0005	0.5232	-0.5345	-0.5055	2.1198	0.3984	-0.2278	-0.3633	0.2701	0.1412	0.6379	-44.4692	45.7164	66.7634
2	4.2862	-0.0454	3.431	5.5562	1.4758	3.1657	-0.5589	-0.5637	-0.1714	1.2321	-0.2957	0.9925	-0.0983	-0.6316	0.2053	1.5207	-0.5605	-0.091	0.8315	0.0834	0.6951	-52.1884	41.3043	77.2433
3	1.1166	-0.7597	-2.2676	4.1152	-1.2317	6.7786	-0.6061	0.8043	0.0571	0.019	0.5818	1.1712	0.3628	-0.9932	-0.3113	0.3978	-0.0013	-0.1474	0.4826	0.0194	0.9851	-53.6617	37.6386	66.7077
4	0.158	-0.2874	0.1951	0.6849	-0.3703	1.4616	0.275	-0.4041	-1.009	-0.057	-0.0732	-0.0996	1.2581	-0.3537	-1.6785	0.8435	-0.5262	-0.5904	-0.0962	-0.0369	0.8804	-44.1632	28.3809	68.4692
5	1.8656	-0.0766	-0.9623	1.5178	-0.159	0.691	0.3542	0.168	-0.7017	-0.1254	-0.0591	-0.2956	0.5484	-0.2897	0.1115	0.4938	-0.0431	-0.2914	0.301	0.0116	0.5512	-35.2531	34.1404	68.261
6	2.0387	-0.0485	1.2154	2.1848	-0.6844	2.3292	0.0866	0.2554	-0.6476	0.0832	0.1052	-0.8457	0.5483	0.5253	-0.0222	0.3443	0.0426	-0.2142	0.2981	0.0619	0.5972	-17.0036	43.1449	72.8728
7	5.7478	-0.5907	0.3814	3.1017	-1.942	1.2587	0.5598	1.0828	-1.081	-1.4767	-0.7509	-0.0267	0.6649	0.4436	0.0389	0.5842	0.2332	-0.1086	0.5568	0.0949	0.3824	-14.8411	46.1702	58.5202
8	0.8178	-0.0266	0.1127	0.8698	0.1004	0.0362	-0.1961	0.4948	-0.215	-0.6016	-0.2092	-0.5637	0.3683	0.844	-0.6255	0.788	0.2895	0.3051	0.8706	0.1664	0.2445	-10.3137	53.5061	50.7596
9	6.9782	-4.3605	3.5981	6.4033	-2.0132	1.7926	-0.1124	0.2839	0.9526	0.6924	-0.1121	-1.9251	-0.2259	0.3731	0.0351	0.5268	0.1121	-0.0297	0.7695	0.1669	0.911	0.1174	45.8384	66.9423
10	1.2578	-1.3892	1.4733	4.1657	-1.5619	2.0636	0.3346	-0.0652	-1.0709	0.0581	-0.7852	-0.7129	1.6843	1.2442	-3.7525	1.3128	0.5014	0.1316	0.5465	0.5422	1.4773	-2.0551	36.4122	67.1559
11	3.981	-2.324	0.9119	2.5541	-2.6327	4.1407	0.2612	0.3514	-0.4266	-0.1774	0.1128	-0.9762	0.3453	0.0635	0.3797	0.7385	0.0413	-0.2237	0.3498	0.0222	0.4734	-13.2439	68.3095	86.3042
12	9.3428	-0.1272	-1.4364	2.1394	2.0168	3.0648	0.4591	0.9064	-0.6197	-1.081	-0.3982	0.15	1.2211	0.0643	-0.0976	1.3776	-0.162	-0.3429	0.6058	0.1712	0.5679	-7.4646	59.9943	95.9995
13	5.006	2.0723	0.3499	1.7745	-0.1551	0.1313	-0.2807	-0.6715	-0.3979	0.3206	0.1093	-0.5515	0.2668	1.5642	0.3517	1.0435	0.1381	-0.329	0.6648	0.021	0.5816	-5.2814	70.4882	95.5494
14	3.7178	1.8051	1.7246	3.8943	0.9319	1.0872	0.3627	-1.2442	-0.1692	1.4172	-0.4024	-0.1263	-0.2915	-0.5975	0.0431	0.8549	-0.2413	-0.5467	0.6943	-0.0649	0.4913	-16.2536	73.0062	102.8075
15	2.2618	1.0779	1.1264	3.8164	1.7318	1.3284	-0.0546	-0.6059	0.4655	0.5753	-0.1463	0.21	-0.2264	-0.4607	0.2077	0.7144	0.0615	-0.1267	0.5003	-0.0893	0.3734	-24.0639	71.9981	95.8457
16	3.5972	1.4797	1.0998	5.3127	-0.7256	1.14	-0.1335	-1.0485	0.6148	0.9276	-0.3247	1.1487	-0.9542	-1.0602	0.0502	0.7144	0.1415	-0.0593	0.6659	-0.1211	0.5398	-41.4072	66.4058	85.7691
17	3.4098	0.9262	0.5135	1.1864	-1.2332	2.3238	-0.0502	-0.9132	1.2542	0.6586	-0.0356	0.2531	-1.5965	-0.593	-0.438	0.9367	0.2036	-0.1918	0.3701	-0.1462	0.7428	-40.8516	78.7791	77.6622
18	0.3174	0.4264	-0.1288	0.5871	-0.0731	0.9585	-0.3715	-0.1483	0.5957	0.2856	0.1841	0.7001	-0.8149	-0.5638	-3.8915	1.0859	0.3316	-0.6253	0.0266	0.1846	0.8247	-42.8449	83.9442	67.4931
19	7.3464	-3.0761	0.6225	3.5949	1.854	2.0313	-1.0973	-2.0698	-0.2962	0.8468	0.2191	0.9803	0.3246	-0.6943	-0.3063	0.8035	0.652	-0.2796	1.3885	-0.0802	1.1958	-56.7442	72.7417	78.1108
20	1.0503	1.3849	-0.0352	2.1643	-0.8702	2.3263	-0.3002	-1.4435	0.6048	1.132	0.3811	1.0697	-0.5428	-0.7323	0.5431	1.2597	0.7116	0.1173	1.5542	-0.0487	0.8769	-55.7889	75.5592	87.2754

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	CHAIN A AND (RESSEQ -1:27)
2	X-RAY DIFFRACTION	2	CHAIN A AND (RESSEQ 28:36)
3	X-RAY DIFFRACTION	3	CHAIN A AND (RESSEQ 37:60)
4	X-RAY DIFFRACTION	4	CHAIN A AND (RESSEQ 61:92)
5	X-RAY DIFFRACTION	5	CHAIN A AND (RESSEQ 93:165)
6	X-RAY DIFFRACTION	6	CHAIN A AND (RESSEQ 172:279)
7	X-RAY DIFFRACTION	7	CHAIN A AND (RESSEQ 280:347)
8	X-RAY DIFFRACTION	8	CHAIN A AND (RESSEQ 348:361)
9	X-RAY DIFFRACTION	9	CHAIN A AND (RESSEQ 362:386)
10	X-RAY DIFFRACTION	10	CHAIN A AND (RESSEQ 387:431)
11	X-RAY DIFFRACTION	11	CHAIN B AND (RESSEQ -1:27)
12	X-RAY DIFFRACTION	12	CHAIN B AND (RESSEQ 28:36)
13	X-RAY DIFFRACTION	13	CHAIN B AND (RESSEQ 37:60)
14	X-RAY DIFFRACTION	14	CHAIN B AND (RESSEQ 61:92)
15	X-RAY DIFFRACTION	15	CHAIN B AND (RESSEQ 93:165)
16	X-RAY DIFFRACTION	16	CHAIN B AND (RESSEQ 172:279)
17	X-RAY DIFFRACTION	17	CHAIN B AND (RESSEQ 280:347)
18	X-RAY DIFFRACTION	18	CHAIN B AND (RESSEQ 348:361)
19	X-RAY DIFFRACTION	19	CHAIN B AND (RESSEQ 362:386)
20	X-RAY DIFFRACTION	20	CHAIN B AND (RESSEQ 387:431)

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