PDB-5je6: Crystal structure of Burkholderia glumae ToxA

ID or keywords:

Entry

Database: PDB / ID: 5je6

Title

Crystal structure of Burkholderia glumae ToxA

Components

Methyl transferase

Keywords

TRANSFERASE / N-methyltransferase / S-adenosylmethionine (SAM) / Apoenzyme / Homooligomer

Function / homology

Function and homology information

methyltransferase activity / methylation
Similarity search - Function

Biological species

Burkholderia glumae (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 1.571 Å

Authors

Fenwick, M.K. / Philmus, B. / Begley, T.P. / Ealick, S.E.

Funding support

United States, 5items

Organization	Grant number	Country
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	GM73220	United States
Robert A. Welch Foundation	A-0034	United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	GM103403	United States
Department of Energy (DOE, United States)	DE-AC02-06CH11357	United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	GM103485	United States

Citation

Journal: Biochemistry / Year: 2016
Title: Burkholderia glumae ToxA Is a Dual-Specificity Methyltransferase That Catalyzes the Last Two Steps of Toxoflavin Biosynthesis.
Authors: Fenwick, M.K. / Philmus, B. / Begley, T.P. / Ealick, S.E.

History

Deposition	Apr 17, 2016	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	May 11, 2016	Provider: repository / Type: Initial release
Revision 1.1	May 25, 2016	Group: Database references
Revision 1.2	Sep 20, 2017	Group: Author supporting evidence / Database references / Derived calculations Category: citation / pdbx_audit_support / pdbx_struct_oper_list Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3	Dec 4, 2019	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4	Mar 6, 2024	Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5je6.cif.gz	224.1 KB	Display	PDBx/mmCIF format
PDB format	pdb5je6.ent.gz	179.5 KB	Display	PDB format
PDBx/mmJSON format	5je6.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/je/5je6 ftp://data.pdbj.org/pub/pdb/validation_reports/je/5je6	HTTPS FTP

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Related structure data

Related structure data	5jdyC 5jdzC 5je0C 5je1C 5je2C 5je3C 5je4C 5je5C C: citing same article (ref.)
Similar structure data	6ry4-d 6sq8-1 5t8u-1 5ttk-3 3fce-d 4mes-d 5v5e-d 5r92-d 2vll-1 3t38-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: Methyl transferase

B: Methyl transferase

hetero molecules

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

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	152.992, 56.424, 60.831
Angle α, β, γ (deg.)	90.00, 91.32, 90.00
Int Tables number	5
Space group name H-M	C121

Components on special symmetry positions

ID	Model	Components
1	1	A-648- HOH
2	1	A-685- HOH
3	1	B-712- HOH
4	1	B-719- HOH

#1: Protein	Methyl transferase / Methyltransferase / Putative ubiquinone/menaquinone biosynthesis methyltransferase / TRP-1 Mass: 27819.277 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Burkholderia glumae (bacteria) / Gene: toxA / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9LBJ0
#2: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂H₆O₂
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 770 / 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: 2.36 Å³/Da / Density % sol: 47.86 % / Description: Plate
Crystal grow	Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 19% polyethylene glycol 3000 and 100 mM sodium citrate, pH 5.5

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.977 Å
Detector	Type: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 9, 2010
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.977 Å / Relative weight: 1
Reflection	Resolution: 1.57→19.4 Å / Num. obs: 69075 / % possible obs: 95.6 % / Redundancy: 3.4 % / R_merge(I) obs: 0.027 / Net I/av σ(I): 34.8 / Net I/σ(I): 21.5
Reflection shell	Resolution: 1.57→1.63 Å / Redundancy: 2.9 % / R_merge(I) obs: 0.215 / Mean I/σ(I) obs: 4.3 / % possible all: 89.3

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Processing

Software

Name	Version	Classification
PHENIX	(1.10-2155-000)	refinement
XDS		data reduction
HKL-2000		data collection
HKL-2000		data scaling
SHELXCD		phasing
AutoSol		phasing

Refinement

Method to determine structure:

SAD / Resolution: 1.571→19.4 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 18.08

	R_factor	Num. reflection	% reflection
R_free	0.1789	3397	4.92 %
R_work	0.1475	-	-
obs	0.1491	69067	95.42 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.571→19.4 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3738	0	22	770	4530

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.016	4052
X-RAY DIFFRACTION	f_angle_d	1.414	5504
X-RAY DIFFRACTION	f_dihedral_angle_d	14.366	2379
X-RAY DIFFRACTION	f_chiral_restr	0.093	553
X-RAY DIFFRACTION	f_plane_restr	0.011	743

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 (%)
1.5705-1.593	0.241	120	0.1832	2290	X-RAY DIFFRACTION	80
1.593-1.6167	0.2194	143	0.181	2587	X-RAY DIFFRACTION	92
1.6167-1.642	0.2293	117	0.1767	2713	X-RAY DIFFRACTION	94
1.642-1.6689	0.2183	147	0.1743	2715	X-RAY DIFFRACTION	95
1.6689-1.6976	0.2184	129	0.18	2733	X-RAY DIFFRACTION	95
1.6976-1.7285	0.2419	132	0.1724	2739	X-RAY DIFFRACTION	95
1.7285-1.7617	0.2353	146	0.1735	2720	X-RAY DIFFRACTION	95
1.7617-1.7977	0.2147	148	0.1705	2697	X-RAY DIFFRACTION	95
1.7977-1.8367	0.1714	141	0.1611	2755	X-RAY DIFFRACTION	96
1.8367-1.8794	0.1859	151	0.1624	2699	X-RAY DIFFRACTION	96
1.8794-1.9264	0.2016	135	0.1613	2752	X-RAY DIFFRACTION	96
1.9264-1.9784	0.1996	140	0.1607	2773	X-RAY DIFFRACTION	96
1.9784-2.0366	0.192	156	0.1593	2742	X-RAY DIFFRACTION	96
2.0366-2.1022	0.1739	160	0.1483	2744	X-RAY DIFFRACTION	96
2.1022-2.1773	0.1935	142	0.1456	2761	X-RAY DIFFRACTION	96
2.1773-2.2643	0.1844	143	0.1422	2762	X-RAY DIFFRACTION	97
2.2643-2.3672	0.19	151	0.145	2763	X-RAY DIFFRACTION	97
2.3672-2.4918	0.1903	153	0.1533	2749	X-RAY DIFFRACTION	97
2.4918-2.6475	0.1997	127	0.1508	2852	X-RAY DIFFRACTION	97
2.6475-2.8513	0.1837	110	0.1485	2842	X-RAY DIFFRACTION	97
2.8513-3.1372	0.1886	150	0.1454	2801	X-RAY DIFFRACTION	97
3.1372-3.5887	0.141	161	0.1329	2806	X-RAY DIFFRACTION	98
3.5887-4.5121	0.1365	162	0.1193	2808	X-RAY DIFFRACTION	98
4.5121-19.4476	0.1685	133	0.1432	2867	X-RAY DIFFRACTION	96

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	2.0973	0.6272	-0.1129	4.8787	5.2629	8.2146	-0.1177	0.3342	-0.1715	-0.2173	-0.1591	-0.127	0.2427	0.4938	0.0995	0.1231	-0.0449	-0.0259	0.2823	0.0809	0.2187	25.9388	21.0822	39.5487
2	5.0268	0.8234	2.0176	2.9884	-0.5881	4.4839	-0.0244	0.0838	-0.0574	0.0533	0.0234	-0.1795	-0.1168	0.2427	-0.0076	0.0793	-0.0098	0.0227	0.102	0.0075	0.0799	15.7172	21.0764	48.2539
3	4.3291	-5.8921	3.8567	8.4647	-4.7023	4.3147	0.2159	0.4741	-0.3531	-0.0123	-0.1639	0.4551	0.7146	0.0753	-0.1231	0.1707	-0.035	-0.0008	0.1682	-0.0102	0.1781	7.6832	10.8694	43.9529
4	0.6423	0.147	0.8615	1.2248	-1.1373	2.4936	-0.0993	-0.1494	0.1094	0.2967	0.2024	0.2554	-0.2818	-0.3407	-0.15	0.1461	0.0385	0.042	0.1816	0.0147	0.1411	5.9335	24.5188	49.5193
5	0.8711	0.0909	-0.6099	2.0718	-0.6583	3.4301	-0.0251	-0.0036	0.0921	0.2602	0.0391	0.0607	-0.3831	-0.0135	-0.0362	0.1253	-0.0238	-0.0025	0.0886	-0.0019	0.1124	13.1449	34.4493	38.1658
6	0.7622	-1.6637	-0.5567	4.7558	1.9177	1.4433	-0.0078	0.0327	-0.0526	0.0651	-0.0243	0.1364	0.0083	0.1074	0.0371	0.1562	-0.0424	-0.0177	0.1371	0.0161	0.1434	14.9562	27.3675	22.4161
7	1.596	-0.2006	-0.1955	2.8561	0.4443	4.2001	-0.1267	0.0507	0.019	0.4108	0.0547	0.02	0.0528	0.0725	0.072	0.1642	-0.0204	0.0034	0.0799	0.0254	0.1182	12.2265	36.8944	32.4312
8	2.6349	0.2069	-0.3461	1.9635	-0.079	2.5079	0.0184	0.1126	-0.1513	0.2413	-0.0444	-0.4488	-0.1081	0.4919	0.0004	0.1435	-0.0681	-0.0646	0.2056	0.0494	0.2173	27.5252	32.2823	34.6975
9	0.931	-0.048	1.1782	9.4601	4.8064	4.3626	-0.0401	-0.0747	0.0678	-0.0259	0.1097	-0.3862	-0.1305	0.2339	-0.0726	0.073	0.008	0.0219	0.2113	0.014	0.1624	25.9998	11.4185	17.2935
10	2.5988	-0.2152	-0.746	3.136	0.4644	3.4611	0.0215	-0.0019	0.0317	-0.0438	-0.0166	-0.0919	-0.0009	0.1372	-0.0159	0.066	0.0248	-0.0042	0.1096	0.0155	0.0728	16.3387	12.3728	8.1437
11	6.8384	2.6798	-3.0341	6.16	-1.6415	6.0846	0.1732	-0.2629	0.0865	-0.0883	-0.1558	0.255	-0.5367	0.0248	-0.0653	0.1682	0.0412	-0.003	0.1084	-0.0254	0.1157	9.406	23.4472	11.7869
12	0.3161	0.0377	-0.3941	1.584	-1.0332	2.0039	0.0236	0.0726	-0.0468	-0.1231	0.1163	0.3047	0.0356	-0.3122	-0.1137	0.0869	-0.0027	-0.0193	0.1604	0.0006	0.1372	7.3746	7.3171	10.9209
13	0.6254	0.4438	0.8723	3.0771	-0.6363	5.0498	0.0357	0.1139	-0.0304	-0.1849	0.2457	0.2869	0.346	-0.5757	-0.1648	0.1249	-0.0563	-0.0566	0.1611	0.0285	0.1939	4.2631	-3.0437	13.4412
14	0.3921	0.4216	0.4168	1.5633	-0.1877	3.6764	0.1058	0.0076	-0.0022	0.1537	0.0341	0.0077	-0.0536	-0.1522	-0.1282	0.1279	0.0463	0.0134	0.0851	0.0102	0.1253	15.8186	0.5262	26.3332
15	6.556	6.7717	1.6266	6.6897	1.6564	0.444	-0.2304	0.1704	0.2942	0.3251	0.4448	0.1786	-0.0758	0.1833	-0.1401	0.2789	0.034	0.0287	0.1624	0.0023	0.1044	12.758	9.7961	33.0826
16	1.777	0.4738	0.2589	6.4549	0.1871	2.3844	-0.1276	-0.0799	0.035	-0.0114	0.1045	0.0906	-0.1892	-0.0837	0.0515	0.0992	0.0098	-0.0126	0.0876	0.0214	0.1	9.9953	-2.3461	24.0689
17	8.9085	6.8018	7.0792	5.73	5.0754	6.3097	-0.181	0.5835	-0.1975	-0.2448	0.3369	-0.3388	0.102	0.544	-0.1478	0.1254	0.0448	0.0104	0.1405	-0.0148	0.1546	25.0179	-2.5303	17.458
18	3.9601	2.1513	3.2765	2.4211	1.8863	3.7846	0.0978	-0.0052	-0.1619	-0.0042	0.119	-0.2993	0.098	0.2667	-0.2523	0.1006	0.0416	-0.0014	0.1422	-0.0062	0.165	26.0876	1.0818	25.717

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 12 through 35 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 36 through 71 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 72 through 85 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 86 through 106 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 107 through 156 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 157 through 184 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 185 through 203 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 204 through 245 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 12 through 35 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 36 through 71 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 72 through 85 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 86 through 119 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 120 through 133 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 134 through 171 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 172 through 184 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 185 through 203 )
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 204 through 222 )
18	X-RAY DIFFRACTION	18	chain 'B' and (resid 223 through 245 )

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