PDB-5ufn: Crystal structure of Burkholderia thailandensis 1,6-didemethyltox...

ID or keywords:

Entry

Database: PDB / ID: 5ufn

Title

Crystal structure of Burkholderia thailandensis 1,6-didemethyltoxoflavin-N1-methyltransferase with bound S-adenosylhomocysteine

Components

Methyltransferase domain protein

Keywords

TRANSFERASE / N-methyltransferase / Complex / S-adenosylmethionine-dependent

Function / homology

Methyltransferase domain / S-adenosyl-L-methionine-dependent methyltransferase superfamily / S-ADENOSYL-L-HOMOCYSTEINE / Uncharacterized protein

Function and homology information

Biological species

Burkholderia thailandensis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

FOURIER SYNTHESIS / Resolution: 1.39 Å

Authors

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

Funding support

United States, 4items

Organization	Grant number	Country
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	GM103403	United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	GM103485	United States
Department of Energy (DOE, United States)	DE-AC02-06CH11357	United States
Oregon State University College of Pharmacy		United States

Citation

Journal: Biochemistry / Year: 2017
Title: Biochemical Characterization and Structural Basis of Reactivity and Regioselectivity Differences between Burkholderia thailandensis and Burkholderia glumae 1,6-Didesmethyltoxoflavin N-Methyltransferase.
Authors: Fenwick, M.K. / Almabruk, K.H. / Ealick, S.E. / Begley, T.P. / Philmus, B.

History

Deposition	Jan 5, 2017	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Dec 13, 2017	Provider: repository / Type: Initial release
Revision 1.1	Dec 26, 2018	Group: Data collection / Database references / Category: citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2	Dec 4, 2019	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3	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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PDBx/mmCIF format	5ufn.cif.gz	209.6 KB	Display	PDBx/mmCIF format
PDB format	pdb5ufn.ent.gz	167.8 KB	Display	PDB format
PDBx/mmJSON format	5ufn.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	5ufn_validation.pdf.gz	995.6 KB	Display	wwPDB validaton report
Full document	5ufn_full_validation.pdf.gz	1000 KB	Display
Data in XML	5ufn_validation.xml.gz	25.3 KB	Display
Data in CIF	5ufn_validation.cif.gz	38.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/uf/5ufn ftp://data.pdbj.org/pub/pdb/validation_reports/uf/5ufn	HTTPS FTP

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Related structure data

Related structure data	5ufmC C: citing same article (ref.)
Similar structure data	3isg-2 6h5g-d 3vnd-6 3vnd-4 5ufm-1 3eis-4 3nb9-d 5x6a-2 3hy6-d 3toi-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

Deposited unit

A: Methyltransferase domain protein

B: Methyltransferase domain protein

hetero molecules

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

1

A: Methyltransferase domain protein

hetero molecules

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

2

B: Methyltransferase domain protein

hetero molecules

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

3

Idetical with deposited unit
defined by software

Unit cell

Length a, b, c (Å)	112.261, 112.261, 78.152
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	169
Space group name H-M	P6₁

#1: Protein	Methyltransferase domain protein / Uncharacterized protein Mass: 26340.449 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Burkholderia thailandensis (strain ATCC 700388 / DSM 13276 / CIP 106301 / E264) (bacteria) Strain: ATCC 700388 / DSM 13276 / CIP 106301 / E264 / Gene: BTH_II1283, DR63_4497 / Plasmid: pET28 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q2T5S0
#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-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: SO₄
#4: Chemical	ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES Mass: 238.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₈H₁₈N₂O₄S / Comment: pH buffer*YM
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 573 / 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: 2.7 Å³/Da / Density % sol: 54.42 %
Crystal grow	Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.4 Details: 100 mM HEPES, pH 6.0 - 7.0, 1.0 - 2.0 M ammonium sulfate, and 1 mM S-adenosylhomocysteine PH range: 6.0 - 7.0

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9793 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 19, 2015
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9793 Å / Relative weight: 1
Reflection	Resolution: 1.39→48.6 Å / Num. obs: 112155 / % possible obs: 99.5 % / Redundancy: 4.9 % / R_merge(I) obs: 0.047 / Net I/av σ(I): 26.9 / Net I/σ(I): 14
Reflection shell	Resolution: 1.39→1.44 Å / Redundancy: 3.7 % / R_merge(I) obs: 0.49 / Mean I/σ(I) obs: 2.24 / CC_1/2: 0.83 / % possible all: 98.1

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Processing

Software

Name	Version	Classification
HKL-2000	v714	data processing
PHENIX	(1.11.1_2575: 000)	refinement
Coot	0.8.7	model building

Refinement

Method to determine structure:

FOURIER SYNTHESIS / Resolution: 1.39→48.6 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 15.84

	R_factor	Num. reflection	% reflection
R_free	0.1679	5521	4.92 %
R_work	0.1479	-	-
obs	0.1489	112141	99.38 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.39→48.6 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3513	0	137	573	4223

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.005	3900
X-RAY DIFFRACTION	f_angle_d	0.942	5351
X-RAY DIFFRACTION	f_dihedral_angle_d	19.851	1424
X-RAY DIFFRACTION	f_chiral_restr	0.083	560
X-RAY DIFFRACTION	f_plane_restr	0.007	704

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 (%)
1.388-1.4038	0.2378	213	0.2201	3258	X-RAY DIFFRACTION	92
1.4038-1.4203	0.216	200	0.2275	3502	X-RAY DIFFRACTION	99
1.4203-1.4376	0.2116	165	0.2021	3583	X-RAY DIFFRACTION	100
1.4376-1.4558	0.2051	187	0.1952	3546	X-RAY DIFFRACTION	100
1.4558-1.4749	0.2105	194	0.1864	3562	X-RAY DIFFRACTION	100
1.4749-1.4952	0.2066	170	0.1848	3561	X-RAY DIFFRACTION	100
1.4952-1.5165	0.1774	155	0.1755	3602	X-RAY DIFFRACTION	100
1.5165-1.5392	0.1961	187	0.1712	3583	X-RAY DIFFRACTION	100
1.5392-1.5632	0.2135	150	0.1609	3574	X-RAY DIFFRACTION	100
1.5632-1.5888	0.1841	190	0.1546	3559	X-RAY DIFFRACTION	100
1.5888-1.6162	0.1745	157	0.1504	3537	X-RAY DIFFRACTION	100
1.6162-1.6456	0.1656	201	0.1531	3589	X-RAY DIFFRACTION	100
1.6456-1.6773	0.187	173	0.1487	3565	X-RAY DIFFRACTION	100
1.6773-1.7115	0.1795	208	0.1469	3530	X-RAY DIFFRACTION	100
1.7115-1.7487	0.1872	200	0.1479	3532	X-RAY DIFFRACTION	100
1.7487-1.7894	0.1684	178	0.1508	3576	X-RAY DIFFRACTION	100
1.7894-1.8342	0.1802	167	0.1535	3588	X-RAY DIFFRACTION	100
1.8342-1.8838	0.1517	178	0.1464	3561	X-RAY DIFFRACTION	100
1.8838-1.9392	0.1697	212	0.1454	3532	X-RAY DIFFRACTION	100
1.9392-2.0018	0.1549	146	0.1408	3618	X-RAY DIFFRACTION	100
2.0018-2.0733	0.1606	215	0.1428	3535	X-RAY DIFFRACTION	100
2.0733-2.1563	0.1521	180	0.1389	3563	X-RAY DIFFRACTION	100
2.1563-2.2545	0.1407	191	0.1328	3569	X-RAY DIFFRACTION	100
2.2545-2.3733	0.1609	207	0.1415	3558	X-RAY DIFFRACTION	100
2.3733-2.522	0.1736	192	0.1485	3566	X-RAY DIFFRACTION	99
2.522-2.7167	0.1883	174	0.1505	3562	X-RAY DIFFRACTION	100
2.7167-2.9901	0.1722	186	0.1521	3596	X-RAY DIFFRACTION	100
2.9901-3.4227	0.1639	189	0.1416	3579	X-RAY DIFFRACTION	99
3.4227-4.3118	0.1421	151	0.1288	3580	X-RAY DIFFRACTION	98
4.3118-48.6403	0.16	205	0.1452	3554	X-RAY DIFFRACTION	97

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	3.5859	-2.2812	-0.0348	5.4843	-0.4662	4.0007	-0.1867	-0.2028	-0.6225	0.3576	0.1416	0.1951	0.4397	-0.419	-0.1113	0.1523	-0.035	0.0106	0.1628	0.0412	0.2241	7.3187	31.1156	26.562
2	1.1154	0.4599	-0.0769	1.3478	0.4197	1.1891	0.0225	0.0432	-0.0788	0.0044	0.0293	-0.0465	0.0538	0.0257	-0.0462	0.0945	0.048	-0.0076	0.1145	-0.0044	0.0956	23.9652	42.6956	18.9151
3	0.5894	0.2128	0.8474	0.3106	-0.1081	2.6797	0.0149	0.0399	-0.1602	-0.0186	0.1003	-0.1232	0.024	0.2751	-0.0875	0.1055	0.0588	0.0051	0.1959	-0.0317	0.1499	34.2054	43.2758	15.1218
4	1.4616	0.1487	0.156	0.9602	0.2712	1.2233	0.0191	-0.1929	-0.1144	0.173	0.0336	-0.0417	0.1364	0.0244	-0.049	0.1283	0.0431	-0.0144	0.1306	0.0235	0.1055	22.0215	38.6699	32.1079
5	2.4978	-0.2962	-0.2633	3.7164	-0.6817	2.3201	-0.0615	0.3978	-0.1732	-0.5998	0.4352	0.2122	-0.3406	-0.4172	-0.3002	0.5647	0.034	0.015	0.3267	0.0936	0.2063	15.6161	79.345	14.8104
6	0.417	-0.0427	0.0003	1.4214	-0.3253	0.8856	-0.0427	-0.0134	0.0112	-0.0123	0.0737	0.1355	-0.085	-0.0912	-0.0399	0.1239	0.0371	-0.0003	0.128	-0.0001	0.1171	11.8829	66.5045	31.9964
7	4.2681	1.5897	-0.4768	7.5488	-1.2373	6.8504	-0.0392	-0.146	-0.0654	0.1529	0.065	0.3641	0.1126	-0.3009	0.0011	0.0804	0.0365	0.0504	0.1407	0.0064	0.1283	4.6832	63.3465	41.6303
8	1.0374	-0.1164	0.2408	1.6138	-0.3641	2.7454	-0.0007	0.0618	0.0842	-0.0607	0.022	-0.0601	-0.1358	0.0162	-0.0217	0.1154	0.0247	0.0082	0.0904	-0.0012	0.1043	20.7704	74.1919	30.9647
9	6.4068	1.2197	0.4671	3.6804	3.4905	3.4472	0.0625	0.2353	0.242	-0.083	0.1112	-0.3126	-0.1417	0.4936	-0.1978	0.1373	0.013	0.022	0.1495	0.0214	0.1805	32.4227	73.9999	29.164
10	3.1989	1.3443	3.5313	3.8049	3.5065	8.5232	0.0708	0.0985	-0.0942	-0.0949	0.108	-0.231	0.0696	0.2256	-0.204	0.0857	0.0189	0.0332	0.0957	0.0073	0.0981	26.7756	64.6215	26.456

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 4 through 24 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 25 through 99 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 100 through 130 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 131 through 228 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 6 through 24 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 25 through 99 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 100 through 117 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 118 through 189 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 190 through 201 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 202 through 228 )

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