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

ID or keywords:

Entry

Database: PDB / ID: 4krg

Title

SeMet Haemonchus contortus Phosphoethanolamine N-methyltransferase 1 in complex with phosphoethanolamine and S-adenosylhomocysteine

Components

Phosphoethanolamine N-methyltransferase 1

Keywords

TRANSFERASE / methyltransferase / phosphoethanolamine / S-adenosylmethionine

Function / homology

Function and homology information

Rossmann fold - #12180 / Methyltransferase domain 25 / Methyltransferase domain / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology

Biological species

Haemonchus contortus (barber pole worm)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.68 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
Revision 1.2	Jul 29, 2020	Group: Data collection / Derived calculations / Structure summary Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id Description: Carbohydrate remediation / Provider: repository / Type: Remediation

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4krg.cif.gz	439 KB	Display	PDBx/mmCIF format
PDB format	pdb4krg.ent.gz	358.7 KB	Display	PDB format
PDBx/mmJSON format	4krg.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4krg_validation.pdf.gz	1.6 MB	Display	wwPDB validaton report
Full document	4krg_full_validation.pdf.gz	1.6 MB	Display
Data in XML	4krg_validation.xml.gz	56.2 KB	Display
Data in CIF	4krg_validation.cif.gz	90.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/kr/4krg ftp://data.pdbj.org/pub/pdb/validation_reports/kr/4krg	HTTPS FTP

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Related structure data

Related structure data	4krhC 4kriC C: citing same article (ref.)
Similar structure data	5cfz-d 4ef9-d 3w76-d 6ze0-2 2ntj-d 2f9r-7 4xsl-1 4oxn-d 3w7l-d 1xx1-2 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 - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#211 - Jul 2017 Pilus Machine similarity (1)

Deposited unit

A: Phosphoethanolamine N-methyltransferase 1

B: Phosphoethanolamine N-methyltransferase 1

hetero molecules

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

1

A: Phosphoethanolamine N-methyltransferase 1

hetero molecules

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

2

B: Phosphoethanolamine N-methyltransferase 1

hetero molecules

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

Unit cell

Length a, b, c (Å)	72.998, 72.998, 360.620
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	170
Space group name H-M	P6₅

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Protein / Sugars , 2 types, 6 molecules AB

#1: Protein

Phosphoethanolamine N-methyltransferase 1

Mass: 54482.125 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Haemonchus contortus (barber pole worm)
Plasmid: pET-28a-HcPMT1 / Production host:

Escherichia coli (E. coli) / Strain (production host): Rosetta II (DE3) / References: UniProt: U5HK46*PLUS

#4: Sugar

ChemComp-BOG / octyl beta-D-glucopyranoside

Type: D-saccharide / Mass: 292.369 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C₁₄H₂₈O₆ / Comment: detergent*YM

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Non-polymers , 4 types, 2041 molecules

#2: Chemical	ChemComp-OPE / PHOSPHORIC ACID MONO-(2-AMINO-ETHYL) ESTER / COLAMINE PHOSPHORIC ACID Mass: 141.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂H₈NO₄P
#3: 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
#5: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 2035 / 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: 2.55 Å³/Da / Density % sol: 51.68 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 0.2 M lithium sulfate monohydrate, 0.1 M Tris-HCl, 30% PEG-4,000, 0.5% n-octyl-beta-D-glucoside, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.979 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 6, 2011 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 twin	Operator: h,-h-k,-l / Fraction: 0.5
Reflection	Resolution: 1.68→47.541 Å / Num. obs: 118707 / % possible obs: 100 % / 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: 1.68→47.541 Å / σ(F): 1.35 / Phase error: 14.11 / Stereochemistry target values: TWIN_LSQ_F

	R_factor	Num. reflection	% reflection
R_free	0.1395	12305	5.04 %
R_work	0.1215	-	-
obs	0.1232	118706	99.91 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.68→47.541 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7570	0	150	2035	9755

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.005	7926
X-RAY DIFFRACTION	f_angle_d	0.987	10758
X-RAY DIFFRACTION	f_dihedral_angle_d	16.988	2954
X-RAY DIFFRACTION	f_chiral_restr	0.07	1200
X-RAY DIFFRACTION	f_plane_restr	0.004	1357

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 (%)
1.68-1.7103	0.2754	607	0.2441	11605	X-RAY DIFFRACTION	95
1.7103-1.7414	0.246	623	0.224	11613	X-RAY DIFFRACTION	95
1.7414-1.7749	0.2352	606	0.2172	11560	X-RAY DIFFRACTION	95
1.7749-1.8111	0.2187	688	0.1957	11483	X-RAY DIFFRACTION	94
1.8111-1.8505	0.193	544	0.1818	11647	X-RAY DIFFRACTION	95
1.8505-1.8936	0.1874	598	0.1719	11659	X-RAY DIFFRACTION	95
1.8936-1.9409	0.1688	606	0.1623	11524	X-RAY DIFFRACTION	95
1.9409-1.9934	0.1548	625	0.1516	11650	X-RAY DIFFRACTION	95
1.9934-2.052	0.1679	621	0.1518	11579	X-RAY DIFFRACTION	95
2.052-2.1182	0.1636	623	0.1464	11600	X-RAY DIFFRACTION	95
2.1182-2.1939	0.1495	630	0.139	11640	X-RAY DIFFRACTION	95
2.1939-2.2817	0.1355	693	0.1331	11555	X-RAY DIFFRACTION	94
2.2817-2.3856	0.1457	659	0.1298	11536	X-RAY DIFFRACTION	95
2.3856-2.5113	0.15	567	0.1247	11675	X-RAY DIFFRACTION	95
2.5113-2.6685	0.1383	631	0.1214	11482	X-RAY DIFFRACTION	95
2.6685-2.8744	0.1361	544	0.1128	11727	X-RAY DIFFRACTION	96
2.8744-3.1635	0.1232	604	0.1034	11685	X-RAY DIFFRACTION	95
3.1635-3.6207	0.1026	637	0.0872	11539	X-RAY DIFFRACTION	95
3.6207-4.5594	0.1002	589	0.0763	11651	X-RAY DIFFRACTION	95
4.5594-31.4938	0.1309	602	0.1116	11569	X-RAY DIFFRACTION	95

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	6.6068	-3.4113	-0.5343	7.0308	-0.1837	4.5594	-0.4142	-0.1917	-0.1574	0.0922	0.1942	-0.1254	0.4095	0.1419	0.2533	0.381	0.135	-0.0952	0.2188	-0.0688	0.2094	-20.3954	81.1402	9.2961
2	4.2969	-0.915	-0.2759	4.0704	0.1511	0.8914	-0.0623	-0.235	0.3262	0.1237	0.1013	-0.3626	-0.6431	0.3286	-0.077	0.4194	-0.0603	0.0057	0.1618	-0.0367	0.1932	-2.6935	63.6778	7.3903
3	0.5959	0.1609	-0.2381	1.168	-0.4692	1.8956	0.0491	0.0888	0.1061	-0.0542	0.0692	0.0349	-0.1779	-0.046	-0.0912	0.1881	0.0212	0.0096	0.1065	0.0206	0.1327	-11.8532	55.3849	-3.209
4	4.4377	0.6067	-1.5795	4.3705	1.6039	4.2344	-0.0218	-1.1431	0.9239	1.1828	0.0135	-0.2257	-0.8961	0.4292	-0.1225	0.567	0.0068	-0.0742	0.3937	-0.1202	0.3731	-2.408	61.9999	19.0792
5	0.7501	-0.1947	-0.3303	1.5226	-0.6258	1.5108	0.0288	0.0393	0.1573	0.0447	0.1425	0.2489	-0.1063	-0.2937	-0.0118	0.1522	0.0437	0.0124	0.1526	0.0536	0.1647	-22.5166	50.701	5.7351
6	1.8525	-0.9472	0.8724	3.3268	-0.5997	0.4261	0.1756	-0.0792	0.1193	0.3626	0.1104	0.4787	-0.4431	-0.5446	-0.0199	0.3119	0.1653	0.1147	0.2585	0.0533	0.2612	-28.7089	55.4117	18.9315
7	0.7327	0.1184	-0.1361	0.5069	-0.3231	1.4175	0.0146	-0.0738	-0.035	0.0511	0.0106	0.0442	0.0981	-0.0278	-0.0332	0.1855	0.0251	0.0045	0.1404	0.0203	0.1133	-19.0512	35.1052	21.0494
8	3.007	0.1669	-1.9328	0.2695	0.3423	1.9321	-0.1757	0.173	-0.2191	0.039	0.0297	0.0256	0.3661	-0.1947	0.1251	0.3019	-0.0201	0.0191	0.1586	0.0066	0.1545	-26.5185	24.1938	14.7112
9	1.0564	0.9433	-0.279	3.9139	2.4987	3.9953	0.0686	-0.0307	-0.0714	0.2368	-0.0324	-0.1104	0.3251	-0.1045	0.003	0.1515	-0.0098	-0.0058	0.1595	0.0427	0.1183	-29.6343	27.7773	29.6428
10	5.0249	-1.5587	-1.8788	4.5893	0.1893	3.7007	-0.1738	-0.0564	0.015	0.1405	-0.0534	-0.05	0.2187	-0.0806	0.1961	0.1833	-0.0414	-0.0309	0.1557	0.0402	0.1008	-31.7866	28.791	27.2543
11	5.9253	-3.3558	3.6301	3.2256	0.5406	7.3267	-0.2001	-0.0511	0.2967	-0.5728	-0.2726	-0.2257	-0.4523	-0.2877	0.5381	0.4414	0.0492	-0.0632	0.1995	0.0157	0.3598	23.5894	5.1405	-15.2957
12	3.3017	0.6405	-0.8723	4.2431	0.6267	2.6477	0.1525	0.2844	0.0544	-0.1357	-0.0737	-0.449	-0.0478	0.5974	-0.0923	0.138	0.0397	0.0075	0.3261	-0.0117	0.1857	17.2043	29.0458	-13.3439
13	0.8908	-0.0815	0.6572	0.7979	-0.012	1.7723	0.0689	-0.0482	-0.0828	0.0463	0.0329	-0.1112	0.1299	0.1343	-0.0721	0.1441	0.0492	-0.0307	0.1545	-0.0069	0.137	5.5055	25.2217	-2.7915
14	1.2592	2.5172	0.3375	8.6259	-0.9809	0.8579	-0.1707	1.1731	-0.2497	-1.0353	-0.4589	0.0223	0.3401	-0.2393	0.3973	0.3279	0.0411	0.0651	0.8315	-0.1208	0.3113	15.497	30.4514	-25.5457
15	1.2386	-0.1848	0.7018	1.2567	-0.0589	1.5776	0.1822	-0.0526	-0.287	0.0271	-0.0037	0.0246	0.2939	-0.0117	-0.0152	0.1941	0.0304	-0.0527	0.1212	0.0081	0.1543	-3.7491	18.6832	-11.9586
16	2.2442	-1.4558	0.6621	1.8918	-1.0563	0.6116	0.2283	0.2637	-0.4072	-0.2901	-0.0058	-0.046	0.4859	0.18	-0.0848	0.3841	0.1183	-0.1148	0.2192	-0.0895	0.2831	-2.8205	10.6122	-25.0806
17	1.1078	0.3816	0.2818	0.7062	0.0045	1.6324	-0.0069	0.0902	0.0071	-0.0855	0.0224	0.022	-0.0628	-0.0943	-0.0146	0.1836	0.0394	-0.0154	0.1601	-0.0032	0.1113	-15.6609	29.1874	-27.0567
18	0.8795	1.5099	0.8072	2.6504	1.7352	1.7958	0.0415	-0.1857	0.0867	0.1512	-0.2029	0.268	0.0378	-0.4018	0.1509	0.1716	0.0458	-0.0024	0.2822	-0.0238	0.1651	-28.7889	28.137	-20.7189
19	2.5878	-0.7775	-1.2388	1.785	1.7264	3.2722	-0.0803	-0.0603	-0.088	-0.055	-0.0224	0.1425	-0.101	-0.1328	0.0944	0.1478	-0.0073	-0.0338	0.2293	0.0037	0.1079	-27.2389	23.6487	-35.719
20	2.7794	0.1391	0.1772	3.9063	1.5575	2.9622	0.0218	-0.0076	-0.1329	-0.0892	-0.0481	0.0751	0.032	-0.1931	0.0569	0.1247	-0.0037	-0.0297	0.2521	0.0129	0.0767	-27.3526	21.1211	-33.0721

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	CHAIN A AND (RESID -5:5)
2	X-RAY DIFFRACTION	2	CHAIN A AND (RESID 6:34)
3	X-RAY DIFFRACTION	3	CHAIN A AND (RESID 35:161)
4	X-RAY DIFFRACTION	4	CHAIN A AND (RESID 162:174)
5	X-RAY DIFFRACTION	5	CHAIN A AND (RESID 175:241)
6	X-RAY DIFFRACTION	6	CHAIN A AND (RESID 242:268)
7	X-RAY DIFFRACTION	7	CHAIN A AND (RESID 269:360)
8	X-RAY DIFFRACTION	8	CHAIN A AND (RESID 361:414)
9	X-RAY DIFFRACTION	9	CHAIN A AND (RESID 415:444)
10	X-RAY DIFFRACTION	10	CHAIN A AND (RESID 445:460)
11	X-RAY DIFFRACTION	11	CHAIN B AND (RESID -5:5)
12	X-RAY DIFFRACTION	12	CHAIN B AND (RESID 6:34)
13	X-RAY DIFFRACTION	13	CHAIN B AND (RESID 35:161)
14	X-RAY DIFFRACTION	14	CHAIN B AND (RESID 162:174)
15	X-RAY DIFFRACTION	15	CHAIN B AND (RESID 175:241)
16	X-RAY DIFFRACTION	16	CHAIN B AND (RESID 242:268)
17	X-RAY DIFFRACTION	17	CHAIN B AND (RESID 269:360)
18	X-RAY DIFFRACTION	18	CHAIN B AND (RESID 361:414)
19	X-RAY DIFFRACTION	19	CHAIN B AND (RESID 415:444)
20	X-RAY DIFFRACTION	20	CHAIN B AND (RESID 445:460)

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Yorodumi