PDB-6fv5: QTRT2, the non-catalytic subunit of murine tRNA-Guanine Transglyc...

ID or keywords:

Entry

Database: PDB / ID: 6fv5

Title

QTRT2, the non-catalytic subunit of murine tRNA-Guanine Transglycosylase

Components

Queuine tRNA-ribosyltransferase accessory subunit 2

Keywords

TRANSFERASE /

Transglycosylase /

TIM barrel

Function / homology

Function and homology information

transferase complex / tRNA-guanosine(34) queuine transglycosylase activity / tRNA-guanine transglycosylation / mitochondrial outer membrane /

tRNA binding / protein heterodimerization activity / protein homodimerization activity / protein-containing complex /

mitochondrion / zinc ion binding /

cytoplasm
Similarity search - Function

Biological species

Mus musculus (house mouse)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.179 Å

Authors

Behrens, C. / Heine, A. / Reuter, K.

Citation

Journal: Biochemistry / Year: 2018
Title: Homodimer Architecture of QTRT2, the Noncatalytic Subunit of the Eukaryotic tRNA-Guanine Transglycosylase.
Authors: Behrens, C. / Biela, I. / Petiot-Becard, S. / Botzanowski, T. / Cianferani, S. / Sager, C.P. / Klebe, G. / Heine, A. / Reuter, K.

History

Deposition	Mar 1, 2018	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jun 13, 2018	Provider: repository / Type: Initial release
Revision 1.1	Jul 11, 2018	Group: Data collection / Database references / Category: citation Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2	May 8, 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	6fv5.cif.gz	304.3 KB	Display	PDBx/mmCIF format
PDB format	pdb6fv5.ent.gz	246.1 KB	Display	PDB format
PDBx/mmJSON format	6fv5.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/fv/6fv5 ftp://data.pdbj.org/pub/pdb/validation_reports/fv/6fv5	HTTPS FTP

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Related structure data

Similar structure data	2pwu-1 4q8u-1 2qzr-1 1p0b-1 3gc4-1 3gc5-1 1s39-1 6h7c-1 5jgo-1 5jt7-1 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: Queuine tRNA-ribosyltransferase accessory subunit 2

B: Queuine tRNA-ribosyltransferase accessory subunit 2

hetero molecules

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

1

Idetical with deposited unit
defined by author&software
Evidence: mass spectrometry, 80 % Homodimer

Unit cell

Length a, b, c (Å)	118.475, 124.573, 61.849
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	18
Space group name H-M	P2₁2₁2

#1: Protein	Queuine tRNA-ribosyltransferase accessory subunit 2 / Queuine tRNA-ribosyltransferase domain-containing protein 1 Mass: 47219.207 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Qtrt2, Qtrtd1 / Plasmid: pASK IBA 13plus / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B8ZXI1
#2: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical	ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₄H₁₀O₃
#4: Chemical	ChemComp-MLI / MALONATE ION / Malonic acid Mass: 102.046 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₂O₄
#5: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 209 / 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: 2.42 Å³/Da / Density % sol: 49.2 %
Crystal grow	Temperature: 291.5 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 100 mmol/l Bis Tris propane pH 6.5 200 mmol/l Sodium malonate 25 % PEG 3350 10 mmol/l Betaine hydrochloride

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Data collection

Diffraction

ID	Mean temperature (K)	Crystal-ID
1	100	1
2	100	1

Diffraction source

Source	Site	Beamline	ID	Wavelength (Å)
SYNCHROTRON	BESSY	14.1	1	0.9184
SYNCHROTRON	BESSY	14.1	2	1.28273

Detector

Type	ID	Detector	Date	Details
DECTRIS PILATUS 6M	1	PIXEL	Nov 24, 2016	sagitally bended Si111-crystal
DECTRIS PILATUS 6M	2	PIXEL	Nov 24, 2016

Radiation

ID	Monochromator	Protocol	Monochromatic (M) / Laue (L)	Scattering type	Wavelength-ID
1	s	SINGLE WAVELENGTH	M	x-ray	1
2		SINGLE WAVELENGTH	M	x-ray	2

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	0.9184	1
2	1.28273	1

Reflection

B_iso Wilson estimate: 35.3 Å² / Entry-ID: 6FV5 / CC_1/2: 0.999

Resolution (Å)	Num. obs	% possible obs (%)	Redundancy (%)	R_sym value	Diffraction-ID	Net I/σ(I)
2.179-50	46914	96.4	6.5	0.079	1	15.56
2.3-50	78969	99.4	13.8	0.083	2	21.9

Reflection shell

Resolution (Å)	Redundancy (%)	Mean I/σ(I) obs	Num. unique obs	R_sym value	Diffraction-ID	% possible all
2.179-2.31	5.3	2.7	6374	0.535	1	82.2
2.3-2.43	13.5	4.38	12669	0.556	2	99

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Processing

Software

Name	Version	Classification
PHENIX	(1.10.1_2155: ???)	refinement
XDS		data reduction
XDS		data scaling
HKL2Map		phasing
Coot		model building

Refinement

Method to determine structure:

SAD / Resolution: 2.179→42.781 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 22.26 / Details: Phenix refinement

	R_factor	Num. reflection	% reflection
R_free	0.2075	1946	4.15 %
R_work	0.1695	-	-
obs	0.1711	46910	96.4 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.179→42.781 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5744	0	16	209	5969

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	5891
X-RAY DIFFRACTION	f_angle_d	0.96	7977
X-RAY DIFFRACTION	f_dihedral_angle_d	13.2	3536
X-RAY DIFFRACTION	f_chiral_restr	0.054	922
X-RAY DIFFRACTION	f_plane_restr	0.006	1025

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 (%)
2.1786-2.2331	0.3056	107	0.2421	2465	X-RAY DIFFRACTION	75
2.2331-2.2935	0.2972	123	0.2173	2860	X-RAY DIFFRACTION	87
2.2935-2.361	0.2308	137	0.2088	3160	X-RAY DIFFRACTION	96
2.361-2.4372	0.2669	142	0.1943	3286	X-RAY DIFFRACTION	100
2.4372-2.5243	0.2421	143	0.1939	3288	X-RAY DIFFRACTION	100
2.5243-2.6253	0.2308	141	0.1959	3279	X-RAY DIFFRACTION	100
2.6253-2.7448	0.2371	141	0.1947	3245	X-RAY DIFFRACTION	98
2.7448-2.8895	0.2618	143	0.1998	3301	X-RAY DIFFRACTION	100
2.8895-3.0705	0.2411	143	0.1953	3323	X-RAY DIFFRACTION	100
3.0705-3.3074	0.2728	143	0.1861	3292	X-RAY DIFFRACTION	99
3.3074-3.6401	0.2157	142	0.1673	3285	X-RAY DIFFRACTION	99
3.6401-4.1665	0.1768	145	0.1378	3351	X-RAY DIFFRACTION	100
4.1665-5.2478	0.1309	145	0.1273	3347	X-RAY DIFFRACTION	99
5.2478-42.7889	0.1823	151	0.1618	3482	X-RAY DIFFRACTION	98

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	5.8496	-3.1827	1.6136	7.8397	-1.4414	5.6886	0.1953	-0.2427	0.1121	0.5162	-0.1734	0.8344	-0.1344	-1.243	-0.1097	0.3894	0.0952	0.0948	0.599	-0.0403	0.3601	51.2768	38.7517	-3.4047
2	6.2331	-3.2887	2.1283	2.2847	-1.9979	6.3957	0.0963	-0.529	-0.5014	0.6158	0.1368	0.3175	0.5028	0.0474	-0.1186	0.5154	-0.0432	0.041	0.3644	0.0204	0.419	64.3439	23.5764	3.6916
3	2.519	-0.2179	-0.4461	4.4686	-1.3473	2.5244	-0.0355	-0.146	-0.2446	-0.2223	0.0612	0.3485	0.0561	-0.1774	-0.0552	0.4122	-0.0438	-0.0044	0.4109	0.0076	0.3529	62.7067	15.2352	-9.3788
4	1.1274	0.2958	-0.1378	2.6048	-0.541	1.5503	-0.0286	0.1015	0.0392	0.0309	0.0691	-0.0213	0.1174	-0.0569	0.0097	0.3285	-0.0085	-0.0113	0.3057	-0.0298	0.288	68.8488	26.3121	-18.7396
5	1.838	0.8173	-0.4869	3.4468	-0.1513	1.3507	-0.0751	0.0174	0.0685	-0.0551	0.0902	0.2035	-0.0189	-0.2567	-0.0942	0.2851	0.002	-0.0307	0.3405	0.0257	0.2591	61.8521	35.9905	-22.2378
6	1.8204	-0.8275	0.2816	1.2346	-0.5412	2.871	-0.092	-0.1971	0.1999	0.1636	0.041	0.0186	-0.3973	-0.2236	0.0775	0.3623	0.0385	0.0203	0.2548	-0.0076	0.2644	66.0735	40.9603	-6.1816
7	3.0448	-1.7774	2.0401	3.0181	-0.3652	3.9135	-0.184	0.3343	0.5761	-0.1105	-0.081	-0.3745	-0.8661	0.2722	0.3109	0.5487	-0.0141	0.0555	0.3128	0.0447	0.3265	76.8274	36.4841	15.327
8	1.9141	-1.0332	2.3359	3.0244	-2.2372	4.7599	-0.0931	-0.0068	0.0869	0.1782	-0.0472	-0.0311	-0.259	-0.1885	0.0888	0.3745	0.0296	0.0657	0.3179	-0.0506	0.2526	69.9009	34.5896	10.8798
9	2.2573	1.5448	0.2215	7.3502	-3.6277	5.2562	0.1031	-0.2118	0.0547	0.2142	-0.0575	0.2022	-0.174	-0.1751	-0.085	0.277	-0.0137	0.0463	0.3065	-0.0554	0.3431	73.2786	3.2889	27.3326
10	1.5403	-2.0259	0.1129	3.4663	0.1687	0.8065	0.0424	-0.0329	0.1221	-0.039	-0.0164	-0.1939	-0.074	0.0082	-0.0405	0.2886	-0.0438	-0.0037	0.2675	-0.033	0.3386	90.7301	12.7523	26.7599
11	1.9356	-1.1412	-0.8308	4.4139	0.9575	1.7736	-0.2015	-0.2785	0.0572	0.3175	0.2045	-0.0425	0.049	0.1712	0.0089	0.3377	0.0135	-0.0188	0.3137	-0.0052	0.2458	94.3388	-0.479	34.015
12	1.964	-0.5098	0.4387	1.3395	-1.1616	2.3644	0.0313	0.0835	-0.2252	0.1361	-0.054	-0.0358	0.2581	0.0966	0.0112	0.3331	-0.0219	0.0183	0.2793	-0.0099	0.3694	83.3938	-5.8291	21.7705
13	3.7494	-1.0262	0.5244	5.2342	-1.1694	6.8332	0.19	0.3785	0.0893	-0.4865	-0.2165	-0.1023	0.0968	0.2452	0.0346	0.3038	-0.0108	-0.0068	0.3529	0.0161	0.2986	69.7807	3.2034	0.8435
14	1.5953	-1.7942	1.9906	7.1566	-4.5538	6.3047	0.1599	0.2182	-0.0259	0.0633	-0.1462	0.0463	0.434	-0.1157	-0.0138	0.2959	-0.097	0.0187	0.3037	-0.0345	0.3228	71.7467	-4.7518	14.9168

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 1 through 34 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 35 through 59 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 60 through 91 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 92 through 156 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 157 through 229 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 230 through 286 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 287 through 353 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 354 through 415 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid -1 through 59 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 60 through 156 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 157 through 229 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 230 through 286 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 287 through 372 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 373 through 415 )

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