PDB-3b0p: tRNA-dihydrouridine synthase from Thermus thermophilus

ID or keywords:

Entry

Database: PDB / ID: 3b0p

Title

tRNA-dihydrouridine synthase from Thermus thermophilus

Components

tRNA-dihydrouridine synthase

Keywords

OXIDOREDUCTASE /

Tim Barrel

Function / homology

Function and homology information

tRNA-dihydrouridine20a synthase activity / tRNA-dihydrouridine20 synthase [NAD(P)+] / tRNA-dihydrouridine20 synthase activity / tRNA dihydrouridine synthesis / tRNA dihydrouridine synthase activity /

Oxidoreductases; Acting on the CH-CH group of donors; With NAD+ or NADP+ as acceptor / FMN binding /

flavin adenine dinucleotide binding /

tRNA binding
Similarity search - Function

Biological species

Thermus thermophilus (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.7 Å

Authors

Yu, F. / Tanaka, Y. / Yamashita, K. / Nakamura, A. / Yao, M. / Tanaka, I.

Citation

Journal: Proc.Natl.Acad.Sci.USA / Year: 2011
Title: Molecular basis of dihydrouridine formation on tRNA
Authors: Yu, F. / Tanaka, Y. / Yamashita, K. / Suzuki, T. / Nakamura, A. / Hirano, N. / Suzuki, T. / Yao, M. / Tanaka, I.

History

Deposition	Jun 12, 2011	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Dec 14, 2011	Provider: repository / Type: Initial release
Revision 1.1	Dec 21, 2011	Group: Database references
Revision 1.2	Oct 11, 2017	Group: Refinement description / Category: software / Item: _software.name
Revision 1.3	Mar 13, 2024	Group: Data collection / Database references / Derived calculations Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3b0p.cif.gz	264.1 KB	Display	PDBx/mmCIF format
PDB format	pdb3b0p.ent.gz	214.9 KB	Display	PDB format
PDBx/mmJSON format	3b0p.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/b0/3b0p ftp://data.pdbj.org/pub/pdb/validation_reports/b0/3b0p	HTTPS FTP

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Related structure data

Related structure data	3b0uC 3b0vC C: citing same article (ref.)
Similar structure data	1l2w-3 6j9h-2 4y83-1 2yer-d 1agw-2 5adw-3 4nz6-1 4egj-3 4rsm-2 1ibq-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 - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: tRNA-dihydrouridine synthase

B: tRNA-dihydrouridine synthase

hetero molecules

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

1

A: tRNA-dihydrouridine synthase

hetero molecules

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

2

B: tRNA-dihydrouridine synthase

hetero molecules

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

Unit cell

Length a, b, c (Å)	42.010, 60.190, 67.000
Angle α, β, γ (deg.)	76.22, 88.67, 70.67
Int Tables number	1
Space group name H-M	P1

#1: Protein	tRNA-dihydrouridine synthase / Mass: 39607.773 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Gene: TTHA0016 / Plasmid: CDFDuet-1 / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: Q5SMC7
#2: Chemical	ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE / Flavin mononucleotide Mass: 456.344 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₇H₂₁N₄O₉P
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 387 / 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: 1.96 Å³/Da / Density % sol: 37.13 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: HEPES, MgCl2, PEG 4000, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å
Detector	Type: ADSC QUANTUM 270 / Detector: CCD / Date: Oct 9, 2010
Radiation	Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 1.7→20 Å / Num. obs: 63578 / % possible obs: 95.6 % / Observed criterion σ(I): -3 / B_iso Wilson estimate: 20.35 Å² / R_sym value: 0.046 / Net I/σ(I): 17.94

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Processing

Software

Name	Version	Classification
PHENIX	dev_777	refinement
PDB_EXTRACT	3.1	data extraction
SERGUI		data collection
XDS		data reduction
XDS		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.7→19.775 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.47 / σ(F): 1.99 / Phase error: 20.29 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2024	4402	7.03 %
R_work	0.1677	-	-
obs	0.1701	62618	94.33 %

Solvent computation

Shrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 49.103 Å² / k_sol: 0.424 e/Å³

Displacement parameters

B_iso mean: 29.86 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	6.1745 Å²	-0.2498 Å²	3.9763 Å²
2-	-	-3.2439 Å²	0.6503 Å²
3-	-	-	-2.9306 Å²

Refinement step

Cycle: LAST / Resolution: 1.7→19.775 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4901	0	62	387	5350

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	5055
X-RAY DIFFRACTION	f_angle_d	1.084	6822
X-RAY DIFFRACTION	f_dihedral_angle_d	13.103	1954
X-RAY DIFFRACTION	f_chiral_restr	0.075	743
X-RAY DIFFRACTION	f_plane_restr	0.006	888

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 (%)
1.697-1.7162	0.29	92	0.2686	1004	X-RAY DIFFRACTION	49
1.7162-1.7364	0.3334	120	0.2624	1774	X-RAY DIFFRACTION	86
1.7364-1.7576	0.3105	131	0.24	1957	X-RAY DIFFRACTION	95
1.7576-1.7798	0.2411	157	0.2227	1958	X-RAY DIFFRACTION	95
1.7798-1.8032	0.2526	153	0.2159	1934	X-RAY DIFFRACTION	95
1.8032-1.8279	0.2481	158	0.2053	1989	X-RAY DIFFRACTION	95
1.8279-1.854	0.2462	141	0.1963	1926	X-RAY DIFFRACTION	95
1.854-1.8816	0.2242	139	0.1953	1966	X-RAY DIFFRACTION	96
1.8816-1.911	0.2222	128	0.1741	2042	X-RAY DIFFRACTION	95
1.911-1.9423	0.2056	157	0.1712	1908	X-RAY DIFFRACTION	95
1.9423-1.9758	0.2083	169	0.1575	1953	X-RAY DIFFRACTION	96
1.9758-2.0117	0.2017	149	0.1567	1989	X-RAY DIFFRACTION	96
2.0117-2.0503	0.2157	148	0.1615	1979	X-RAY DIFFRACTION	96
2.0503-2.0921	0.203	157	0.164	1991	X-RAY DIFFRACTION	96
2.0921-2.1376	0.2013	129	0.1569	1926	X-RAY DIFFRACTION	96
2.1376-2.1872	0.2138	155	0.1517	2005	X-RAY DIFFRACTION	96
2.1872-2.2419	0.2019	157	0.1666	2008	X-RAY DIFFRACTION	97
2.2419-2.3024	0.1851	144	0.1548	1950	X-RAY DIFFRACTION	96
2.3024-2.37	0.1909	150	0.1521	2015	X-RAY DIFFRACTION	97
2.37-2.4464	0.1863	150	0.166	1986	X-RAY DIFFRACTION	97
2.4464-2.5337	0.201	154	0.1603	1973	X-RAY DIFFRACTION	97
2.5337-2.6349	0.2227	139	0.1614	2037	X-RAY DIFFRACTION	97
2.6349-2.7545	0.2122	165	0.1639	1964	X-RAY DIFFRACTION	97
2.7545-2.8993	0.1894	156	0.1642	1998	X-RAY DIFFRACTION	97
2.8993-3.0803	0.1925	147	0.1671	2002	X-RAY DIFFRACTION	98
3.0803-3.3171	0.1802	161	0.1633	2014	X-RAY DIFFRACTION	98
3.3171-3.6491	0.1984	147	0.1573	2016	X-RAY DIFFRACTION	98
3.6491-4.1728	0.1777	159	0.1508	2023	X-RAY DIFFRACTION	98
4.1728-5.241	0.1761	141	0.1489	2028	X-RAY DIFFRACTION	98
5.241-19.776	0.2282	149	0.206	1901	X-RAY DIFFRACTION	93

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	1.6218	0.7186	1.1049	2.1529	0.2914	3.3022	0.0012	-0.0443	-0.1231	-0.0607	0.028	-0.0734	-0.034	-0.0296	-0.0139	0.1358	0.0077	0.0237	0.1321	0.0047	0.1314	64.0415	72.6982	11.1045
2	2.3252	0.6836	0.6163	3.4557	0.3891	3.0658	0.0052	0.1165	0.0326	-0.1673	0.0333	0.1761	0.0063	0.0035	-0.0306	0.1239	-0.0141	0.0054	0.1127	-0.0062	0.119	62.5749	67.1785	-1.5449
3	3.5846	-0.0303	-0.8444	3.1006	-0.311	5.2462	0.4443	-0.0909	-0.3709	-0.0298	0.1333	1.0017	0.714	-1.2722	-0.3011	0.3425	-0.0908	-0.0429	0.3549	0.0887	0.4525	57.3584	52.7533	2.7909
4	1.7279	-0.181	0.7956	4.9807	-1.2526	3.164	-0.0095	-0.015	-0.5051	0.0981	0.143	0.4535	0.6588	-0.3829	0.0118	0.2389	-0.0141	0.0188	0.1094	0.0119	0.2522	63.9108	50.3364	11.2936
5	1.3879	-0.687	-0.2659	2.8812	-0.3388	2.3702	-0.0463	-0.168	-0.2062	0.133	0.0511	0.0166	0.2804	-0.0497	0.0099	0.1436	-0.0078	-0.0009	0.1568	0.033	0.1351	65.7827	60.1267	20.766
6	5.0341	-2.6297	0.2868	7.0827	0.7348	1.0958	-0.0727	-0.6081	0.5637	0.5415	-0.0006	-0.6553	-0.1933	0.2519	0.0594	0.1703	-0.0433	-0.0477	0.2783	-0.0508	0.2538	75.0722	78.0155	22.5115
7	2.5297	-1.1581	2.684	2.0977	-1.8677	8.1833	-0.0719	0.0646	0.2791	0.0889	0.0303	-0.1804	-0.5238	0.1995	0.0188	0.1775	0.0148	0.0274	0.1364	-0.0018	0.1811	62.7782	89.9979	10.4007
8	2.0702	0.1897	1.5618	1.7812	-0.355	5.7862	-0.0348	-0.2226	0.0546	0.3293	0.0834	0.1399	-0.225	-0.0795	-0.0313	0.1734	0.0463	0.039	0.1843	-0.0109	0.1854	55.4885	84.912	16.9946
9	5.3835	0.1655	0.9896	3.0602	-1.2084	5.6486	-0.146	-0.4503	0.6923	0.618	-0.1286	0.3151	-0.8802	-0.2873	0.1981	0.3918	0.1202	0.125	0.195	-0.034	0.2938	55.2903	93.4964	20.5494
10	2.296	-0.6491	-1.1133	2.1954	-0.4751	1.733	-0.0939	0.0245	0.1143	-0.0267	0.0226	-0.0585	-0.0502	-0.0765	0.0729	0.1001	-0.0078	-0.0259	0.1087	-0.0199	0.1162	53.6576	50.263	46.8716
11	2.9429	-0.9344	-0.51	2.5439	-0.2967	2.2997	-0.0313	0.0174	-0.1453	0.062	-0.0517	0.1712	-0.0088	-0.052	0.0801	0.0932	0.0053	-0.0214	0.1218	-0.0088	0.1095	43.3814	54.3274	55.2829
12	2.856	-0.954	-1.2959	3.8409	-0.7137	6.3432	0.1125	0.9435	0.1645	-0.6451	0.0469	0.8725	0.02	-1.4328	0.0459	0.2924	0.0575	-0.0482	0.3557	0.0003	0.346	39.2552	67.6821	47.4577
13	1.1919	0.2232	-0.5279	2.3717	0.0711	2.0417	0.0221	0.1838	0.1761	-0.1812	0.0013	0.0187	-0.3295	-0.0603	-0.0314	0.1538	-0.0123	-0.0318	0.1689	0.0298	0.1303	55.7479	65.8918	41.2104
14	0.9789	0.603	-0.0604	1.8917	0.127	1.525	-0.0743	0.0695	-0.134	-0.0166	0.0141	-0.3461	0.1745	0.2506	0.0231	0.0821	0.0191	-0.009	0.1445	0.0014	0.1418	58.6479	38.4081	43.6345
15	5.2064	0.352	-0.5159	3.2584	-0.0177	3.5805	-0.1097	0.5638	-0.6764	-0.4354	-0.1206	-0.4951	0.6992	0.3273	0.1073	0.2924	0.0322	0.0336	0.2781	-0.0751	0.2497	57.814	28.7972	34.6479

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resseq 2:38)
2	X-RAY DIFFRACTION	2	chain 'A' and (resseq 39:91)
3	X-RAY DIFFRACTION	3	chain 'A' and (resseq 92:124)
4	X-RAY DIFFRACTION	4	chain 'A' and (resseq 125:155)
5	X-RAY DIFFRACTION	5	chain 'A' and (resseq 156:235)
6	X-RAY DIFFRACTION	6	chain 'A' and (resseq 236:250)
7	X-RAY DIFFRACTION	7	chain 'A' and (resseq 251:268)
8	X-RAY DIFFRACTION	8	chain 'A' and (resseq 269:288)
9	X-RAY DIFFRACTION	9	chain 'A' and (resseq 289:318)
10	X-RAY DIFFRACTION	10	chain 'B' and (resseq 2:38)
11	X-RAY DIFFRACTION	11	chain 'B' and (resseq 39:91)
12	X-RAY DIFFRACTION	12	chain 'B' and (resseq 92:124)
13	X-RAY DIFFRACTION	13	chain 'B' and (resseq 125:237)
14	X-RAY DIFFRACTION	14	chain 'B' and (resseq 238:288)
15	X-RAY DIFFRACTION	15	chain 'B' and (resseq 289:319)

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