PDB-5je0: Crystal structure of Burkholderia glumae ToxA with bound S-adenos...

ID or keywords:

Entry

Database: PDB / ID: 5je0

Title

Crystal structure of Burkholderia glumae ToxA with bound S-adenosylhomocysteine (SAH) and 1,6-didemethyltoxoflavin

Components

Methyl transferase

Keywords

TRANSFERASE / N-methyltransferase / S-adenosylmethionine (SAM) / Substrate / Complex

Function / homology

Methyltransferase domain 25 / Methyltransferase domain / methyltransferase activity / methylation / S-adenosyl-L-methionine-dependent methyltransferase superfamily / pyrimido[5,4-e][1,2,4]triazine-5,7(6H,8H)-dione / S-ADENOSYL-L-HOMOCYSTEINE / Methyltransferase

Function and homology information

Biological species

Burkholderia glumae (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.552 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 4, 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 ...Author supporting evidence / Database references / Derived calculations / Structure summary Category: citation / pdbx_audit_support ...citation / pdbx_audit_support / pdbx_struct_oper_list / struct_keywords Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization ..._citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation / _struct_keywords.pdbx_keywords
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
Revision 1.5	Apr 3, 2024	Group: Refinement description / Category: pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	5je0.cif.gz	226 KB	Display	PDBx/mmCIF format
PDB format	pdb5je0.ent.gz	181 KB	Display	PDB format
PDBx/mmJSON format	5je0.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	5je0_validation.pdf.gz	984 KB	Display	wwPDB validaton report
Full document	5je0_full_validation.pdf.gz	986.4 KB	Display
Data in XML	5je0_validation.xml.gz	28.1 KB	Display
Data in CIF	5je0_validation.cif.gz	43.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/je/5je0 ftp://data.pdbj.org/pub/pdb/validation_reports/je/5je0	HTTPS FTP

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Related structure data

Related structure data	5jdyC 5jdzC 5je1C 5je2C 5je3C 5je4C 5je5C 5je6C C: citing same article (ref.)
Similar structure data	5jdz-2 5je4-1 5je1-2 5je2-2 6kbu-1 5h6g-2 5aby-1 5jdy-1 4gux-1 4ue9-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

Deposited unit

A: Methyl transferase

B: Methyl transferase

hetero molecules

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

1

A: Methyl transferase

hetero molecules

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

2

B: Methyl transferase

hetero molecules

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

Unit cell

Length a, b, c (Å)	46.857, 78.558, 144.315
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#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-SAH / S-ADENOSYL-L-HOMOCYSTEINE Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₄H₂₀N₆O₅S
#3: Chemical	ChemComp-AZ8 / pyrimido[5,4-e][1,2,4]triazine-5,7(6H,8H)-dione / 1,6-didemethyltoxoflavin Mass: 165.110 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₅H₃N₅O₂
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 757 / 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: 2.39 Å³/Da / Density % sol: 48.47 % / Description: Plate
Crystal grow	Temperature: 295 K / Method: vapor diffusion, hanging drop Details: 18 - 23% polyethylene glycol monomethyl ether 2000 , 100 mM Tris, pH 6.1 - 6.8, 6 mM SAH, and 10 mM 1,6-didemethyltoxoflavin PH range: 6.1 - 6.8

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.9759 Å
Detector	Type: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 5, 2012
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9759 Å / Relative weight: 1
Reflection	Resolution: 1.55→17.7 Å / Num. obs: 76116 / % possible obs: 98 % / Redundancy: 4.2 % / R_merge(I) obs: 0.081 / Net I/av σ(I): 17.1 / Net I/σ(I): 10
Reflection shell	Resolution: 1.55→1.61 Å / Redundancy: 4 % / R_merge(I) obs: 0.456 / Mean I/σ(I) obs: 3 / % possible all: 100

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Processing

Software

Name	Version	Classification
PHENIX	(1.10-2155-000)	refinement
HKL-2000		data reduction
HKL-2000		data scaling
PHENIX		phasing
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: Burkholderia glumae ToxA

Resolution: 1.552→17.7 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 26.76

	R_factor	Num. reflection	% reflection
R_free	0.2477	3669	4.88 %
R_work	0.2063	-	-
obs	0.2083	75116	96.52 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.552→17.7 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3834	0	76	757	4667

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	4094
X-RAY DIFFRACTION	f_angle_d	0.976	5562
X-RAY DIFFRACTION	f_dihedral_angle_d	13.313	2376
X-RAY DIFFRACTION	f_chiral_restr	0.06	564
X-RAY DIFFRACTION	f_plane_restr	0.006	734

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 (%)
1.552-1.5724	0.3248	144	0.2516	2538	X-RAY DIFFRACTION	92
1.5724-1.594	0.2843	150	0.2328	2809	X-RAY DIFFRACTION	100
1.594-1.6167	0.2665	146	0.2203	2821	X-RAY DIFFRACTION	100
1.6167-1.6408	0.2729	145	0.2172	2791	X-RAY DIFFRACTION	100
1.6408-1.6665	0.2907	133	0.2155	2832	X-RAY DIFFRACTION	100
1.6665-1.6938	0.2392	129	0.21	2822	X-RAY DIFFRACTION	100
1.6938-1.7229	0.2562	162	0.2099	2798	X-RAY DIFFRACTION	100
1.7229-1.7542	0.2647	148	0.2001	2783	X-RAY DIFFRACTION	100
1.7542-1.788	0.2741	141	0.2064	2834	X-RAY DIFFRACTION	100
1.788-1.8244	0.2587	158	0.2346	2798	X-RAY DIFFRACTION	100
1.8244-1.864	0.3503	118	0.3246	2685	X-RAY DIFFRACTION	95
1.864-1.9074	0.3427	113	0.3739	2524	X-RAY DIFFRACTION	89
1.9074-1.955	0.4234	142	0.3797	2805	X-RAY DIFFRACTION	99
1.955-2.0078	0.3157	123	0.2476	2721	X-RAY DIFFRACTION	96
2.0078-2.0668	0.2229	144	0.1881	2812	X-RAY DIFFRACTION	100
2.0668-2.1334	0.2111	168	0.1864	2850	X-RAY DIFFRACTION	100
2.1334-2.2095	0.3011	149	0.2316	2618	X-RAY DIFFRACTION	94
2.2095-2.2978	0.3425	136	0.3056	2780	X-RAY DIFFRACTION	97
2.2978-2.4021	0.2709	148	0.2306	2743	X-RAY DIFFRACTION	96
2.4021-2.5284	0.2136	132	0.1782	2861	X-RAY DIFFRACTION	100
2.5284-2.6863	0.1952	143	0.1752	2864	X-RAY DIFFRACTION	100
2.6863-2.8929	0.2178	146	0.1686	2871	X-RAY DIFFRACTION	100
2.8929-3.1825	0.1967	160	0.1659	2873	X-RAY DIFFRACTION	100
3.1825-3.6396	0.2162	155	0.1581	2768	X-RAY DIFFRACTION	96
3.6396-4.5724	0.1898	78	0.1362	1968	X-RAY DIFFRACTION	73
4.5724-17.7225	0.1907	158	0.1631	2878	X-RAY DIFFRACTION	94

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	0.7123	1.2664	1.6967	3.074	1.8125	5.9061	0.0309	0.6812	0.4472	-0.3024	-0.4651	0.5068	-0.2989	-0.492	0.4089	0.2677	0.0843	-0.1122	0.6737	0.0156	0.399	20.5585	48.5159	78.5176
2	1.7484	-0.0682	0.9992	0.9178	0.3506	0.9494	0.0221	0.4971	-0.0539	-0.0036	-0.2385	0.1349	0.2194	-0.3852	0.1701	0.1893	-0.0612	0.0302	0.4326	-0.1201	0.1922	17.0025	32.5604	78.9257
3	7.4283	3.1283	6.5771	4.5761	1.1863	7.3552	-0.6535	0.5034	0.5035	-0.1914	0.1249	-0.036	-0.4935	-0.213	0.4523	0.1581	0.0393	-0.0105	0.4887	-0.0415	0.2382	8.4657	45.1005	82.6271
4	1.0535	-0.229	0.9532	1.0132	-0.2319	1.1426	-0.0385	0.0186	-0.0466	0.0717	-0.0359	0.0939	0.2213	-0.4708	0.0578	0.1878	-0.0693	0.0517	0.3938	-0.1075	0.2036	13.3686	34.2475	91.9936
5	2.4416	0.5831	0.1865	1.6449	0.7105	2.6366	-0.0435	0.319	0.1556	0.0324	-0.0295	0.0906	0.0796	0.0948	0.0541	0.1141	-0.0035	-0.0034	0.2285	-0.0121	0.1126	31.6485	38.4481	86.0219
6	0.8073	-0.068	0.0785	0.7959	1.3489	2.2048	0.0022	0.6899	-0.2057	-0.0786	0.0109	0.0787	0.1681	0.2688	0.0699	0.1884	-0.0051	0.0102	0.5318	-0.0699	0.1432	32.9868	31.6665	73.7643
7	1.7492	0.4938	-0.6775	3.4549	-1.1465	2.9612	0.0446	-0.1752	0.203	0.186	-0.1473	-0.0781	-0.2709	0.0371	0.0759	0.0656	0.0118	-0.039	0.0973	0.003	0.1279	24.5448	41.6052	50.5256
8	1.8349	-0.3579	0.6142	3.2416	-0.1833	1.4638	-0.0332	-0.0631	-0.0986	0.0302	-0.0297	-0.0879	0.2118	0.3184	0.0382	0.1032	0.0384	0.0175	0.0922	0.041	0.1418	33.3366	32.5444	44.8146
9	4.5485	-3.5479	4.5004	5.2437	-2.434	5.0136	-0.3047	0.1199	0.3306	0.1081	0.0345	-0.1213	-0.4188	0.3733	0.2264	0.1323	-0.0406	0.0303	0.161	0.0403	0.1818	38.4723	45.0937	43.9139
10	1.6189	1.0036	1.062	1.4916	0.1475	2.562	-0.1524	0.355	-0.1121	-0.0684	0.1432	-0.0819	0.0715	0.2941	0.0224	0.1238	0.0305	0.0381	0.1584	0.0134	0.1284	33.4923	34.5102	34.4997
11	1.7328	-0.3915	0.0316	1.3716	0.0795	1.4892	-0.0102	0.0141	0.0928	-0.0989	0.0075	0.0367	-0.0109	-0.1269	-0.0002	0.0923	-0.0026	-0.0123	0.0641	0.0184	0.0933	15.1053	39.1139	40.4195
12	1.9414	0.1368	0.1686	3.2403	3.0189	2.8055	-0.0523	-0.256	-0.1806	0.4053	-0.1242	0.1112	0.9043	-0.1464	0.1179	0.1589	-0.0015	-0.001	0.1343	0.0326	0.1393	15.4446	27.6896	50.7318
13	1.9911	-0.1085	0.0021	2.4025	1.1559	3.9832	-0.0172	-0.4961	-0.0433	0.282	0.1379	0.0466	0.1027	-0.4215	-0.0383	0.1411	0.0264	0.0001	0.1859	0.0327	0.1128	12.1963	35.4059	54.3689

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 5 through 21 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 22 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 203 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 204 through 245 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 5 through 35 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 36 through 71 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 72 through 85 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 86 through 106 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 107 through 203 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 204 through 222 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 223 through 245 )

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