PDB-9qw7: The crystal structure of the adenyly transferase domain of Candid...

ID or keywords:

Entry

Database: PDB / ID: 9qw7

Title

The crystal structure of the adenyly transferase domain of Candida glabrata tRNA ligase

Components

tRNA ligase

Keywords

LIGASE / tRNA ligase

Function / homology

Function and homology information

GTP-dependent polyribonucleotide 5'-hydroxyl-kinase activity / RNA ligase (ATP) / RNA ligase (ATP) activity / tRNA splicing, via endonucleolytic cleavage and ligation / phosphoric diester hydrolase activity / ATP binding / nucleus
Similarity search - Function

Biological species

Nakaseomyces glabratus (fungus)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.75 Å

Authors

McEwen, A.G. / Poussin-Courmontagne, P. / Giovinazzo, A. / Tocchini-Valentini, G.D. / Tocchini-Valentini, G.P. / Pellegrini, M. / Merolle, M.

Funding support

France,

Italy, European Union, 7items

Organization	Grant number	Country
Instruct-ERIC Center (Strasbourg Centre)	PID 222	France
Agence Nationale de la Recherche (ANR)	ANR-10-INBS-000	France
Ministero dell Universita e della Ricerca	PRIN Cofin	Italy
Ministero dell Universita e della Ricerca	DSB AD009	Italy
European Union (EU)	EURASNET	European Union
European Union (EU)	EMMA-Infrafrontier	European Union
European Union (EU)	EUMODIC	European Union

Citation

Journal: Nar Mol Med / Year: 2025
Title: The adaptability of the fungal tRNA ligase's ATP-binding pocket: a potential target for new antifungal drugs.
Authors: McEwen, A.G. / Giovinazzo, A. / Poussin-Courmontagne, P. / Merolle, M. / Tocchini-Valentini, G.P. / Pellegrini, M. / Tocchini-Valentini, G.D.

History

Deposition	Apr 14, 2025	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Sep 17, 2025	Provider: repository / Type: Initial release
Revision 1.1	Dec 10, 2025	Group: Database references / Category: citation / citation_author Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9qw7.cif.gz	318.1 KB	Display	PDBx/mmCIF format
PDB format	pdb9qw7.ent.gz	260.6 KB	Display	PDB format
PDBx/mmJSON format	9qw7.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/qw/9qw7 ftp://data.pdbj.org/pub/pdb/validation_reports/qw/9qw7	HTTPS FTP

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Related structure data

Similar structure data	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
Related items in Molecule of the Month	#129 - Sep 2010 Isocitrate Dehydrogenase similarity (1) #154 - Oct 2012 Citric Acid Cycle similarity (1) #24 - Dec 2001 Glycogen Phosphorylase similarity (1) #55 - Jul 2004 DNA Ligase similarity (1) #16 - Apr 2001 Aminoacyl-tRNA Synthetases similarity (1)

Deposited unit

A: tRNA ligase

B: tRNA ligase

hetero molecules

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

1

A: tRNA ligase

hetero molecules

defined by author
Evidence: gel filtration
45 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: tRNA ligase

hetero molecules

defined by author
Evidence: gel filtration
45 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	81.796, 81.796, 286.593
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	154
Space group name H-M	P3₂21

#1: Protein	tRNA ligase Mass: 44630.211 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: Adenylyl transferase domain / Source: (gene. exp.) Nakaseomyces glabratus (fungus) / Gene: CAGL0M03091g / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): Rosetta / References: UniProt: Q6FJW3, RNA ligase (ATP)
#2: Chemical	ChemComp-AMP / ADENOSINE MONOPHOSPHATE Mass: 347.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₀H₁₄N₅O₇P / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP*YM
#3: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 33 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y
Has protein modification	N

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 3.2 Å³/Da / Density meas: 61.6 Mg/m³ / Density % sol: 60.33 %
Crystal grow	Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 25% PEG 8000, 100mM MES6KOH, 2.5mM MgCl2

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

SOLEIL

/ Beamline: PROXIMA 2 / Wavelength: 0.9801 Å

Detector

Type: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 11, 2014

Radiation

Monochromator: Cryogenically cooled channel cut crystal (Si 111)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.9801 Å / Relative weight: 1

Reflection

Resolution: 2.75→95.531 Å / Num. obs: 15312 / % possible obs: 51.3 % / Redundancy: 3.65 % / CC_1/2: 0.9939 / R_merge(I) obs: 0.119 / R_pim(I) all: 0.07 / R_rim(I) all: 0.139 / Net I/σ(I): 3.411

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. unique obs	CC_1/2	R_pim(I) all	R_rim(I) all	% possible all
2.754-3.119	5.57	1.346	1.587	766	0.5556	0.62	1.486	8.4
3.119-3.309	4.6562	0.654	2.212	765	0.8273	0.33	0.735	23.25
3.31-3.507	3.78	0.46	2.227	766	0.8797	0.254	0.529	28.31
3.507-3.687	3.47	0.36	2.405	765	0.9264	0.206	0.417	38.25
3.687-3.783	3.67	0.357	2.317	766	0.9353	0.212	0.417	82.54
3.783-3.874	3.39	0.345	2.289	766	0.9364	0.209	0.405	96.84
3.874-4.011	3.27	0.277	2.391	765	0.9659	0.17	0.327	73.98
4.011-4.121	3.62	0.217	3.103	766	0.9706	0.132	0.255	100
4.122-4.246	3.59	0.169	3.324	765	0.9784	0.102	0.198	100
4.246-4.389	3.61	0.146	3.54	766	0.9878	0.088	0.171	99.74
4.389-4.547	3.54	0.14	3.573	766	0.9888	0.086	0.165	100
4.547-4.738	3.57	0.114	3.93	765	0.9893	0.07	0.134	99.74
4.739-4.967	3.61	0.102	4.002	766	0.992	0.06	0.119	100
4.967-5.234	3.52	0.106	4.146	765	0.9912	0.062	0.124	99.61
5.234-5.577	3.48	0.119	4.116	766	0.9839	0.073	0.141	100
5.577-6.026	3.46	0.106	4.164	766	0.9917	0.062	0.123	99.61
6.026-6.662	3.46	0.093	4.361	765	0.9918	0.055	0.109	99.87
6.662-7.688	3.36	0.067	4.582	766	0.996	0.042	0.08	100
7.693-9.824	3.32	0.057	5.006	765	0.9962	0.035	0.068	99.87
9.829-95.531	3.02	0.054	4.954	765	0.9919	0.036	0.066	99.74

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Processing

Software

Name	Version	Classification
PHENIX	(1.21rc1_5015: ???)	refinement
XDS		data scaling
XDS		data reduction
PHASER		phasing
PDB_EXTRACT		data extraction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.75→63.5 Å / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 27.95 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2625	703	4.59 %
R_work	0.2177	-	-
obs	0.2198	15302	51.26 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 2.75→63.5 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6065	0	48	33	6146

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.002	6246
X-RAY DIFFRACTION	f_angle_d	0.526	8419
X-RAY DIFFRACTION	f_dihedral_angle_d	12.916	2315
X-RAY DIFFRACTION	f_chiral_restr	0.04	893
X-RAY DIFFRACTION	f_plane_restr	0.003	1080

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 (%)
2.75-2.97	0.5088	22	0.3786	272	X-RAY DIFFRACTION	5
2.97-3.26	0.3179	59	0.3251	995	X-RAY DIFFRACTION	18
3.27-3.74	0.3697	108	0.2699	1988	X-RAY DIFFRACTION	36
3.74-4.71	0.2566	187	0.2119	5439	X-RAY DIFFRACTION	95
4.71-63.5	0.2432	327	0.2045	5905	X-RAY DIFFRACTION	100

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	0.0881	-0.1087	-0.146	0.1571	0.1769	0.2362	-0.0099	-0.1045	-0.0649	0.0429	0.1338	0.0947	0.0855	0.0445	0.0559	0.4989	0.171	0.035	0.2518	-0.0317	0.805	36.2705	-48.7897	17.0767
2	0.4327	-0.066	0.2451	0.0289	0.0674	0.7638	0.169	0.0907	-0.0829	0.0398	0.1574	-0.1466	0.1012	0.232	0.738	0.105	0.0289	0.0626	0.087	-0.0957	0.3451	37.1562	-42.3966	8.7254
3	0.0658	0.0327	0.0012	0.0171	-0.0003	0.0003	0.0908	0.0062	-0.0007	-0.0356	0.0042	-0.0948	-0.0443	0.0156	0.0367	0.5428	0.0511	-0.0748	0.1753	-0.1121	0.5026	21.7393	-49.1372	6.5846
4	-0.0004	-0.0003	-0	0.0175	0.0046	0.0079	0.1466	-0.0009	-0.1309	0.1169	0.2349	-0.0177	0.0302	0.002	0.0002	0.2641	-0.0063	-0.0292	0.2769	-0.0668	0.378	8.701	-39.1143	7.8043
5	0.2349	0.0478	0.1698	0.0111	0.0344	0.1255	-0.1373	-0.1663	0.1765	0.015	0.0287	-0.0118	-0.2029	-0.1384	-0.047	0.253	0.101	0.0265	0.1465	0.0057	0.1893	14.2411	-29.5664	9.9891
6	0.0664	0.0773	-0.092	0.2641	-0.0102	0.2268	-0.0253	0.0895	0.113	0.0287	-0.1316	-0.0485	-0.0057	0.0663	-0.4159	0.271	-0.1631	-0.001	0.2893	0.0976	0.2954	32.7316	-29.1284	8.5182
7	0.12	0.0046	0.0299	0.1248	0.0186	0.0644	-0.0353	0.0662	0.1045	-0.1029	-0.0345	-0.0493	0.0869	0.0009	-0.2527	0.6528	-0.4044	0.1919	0.5587	-0.0119	0.4545	40.4696	-21.7467	2.0074
8	0.0975	-0.0573	-0.0527	0.0336	0.0312	0.0295	0.0461	-0.0702	-0.0405	-0.0094	0.0814	-0.2025	0.0095	0.0006	0.1174	0.3376	-0.2407	-0.0924	0.281	0.0405	0.3945	41.0119	-24.7857	17.0376
9	0.0054	-0.0035	0.0027	0.0016	0.0002	0.0072	0.009	0.0157	0.1638	-0.073	-0.0581	0.1456	0.0473	0.0078	0	0.7889	-0.1316	-0.0904	0.4735	-0.0137	0.5325	25.4261	-21.699	-8.4528
10	0.0294	-0.0566	-0.0977	0.1185	0.1272	0.7381	-0.0196	-0.0414	0.0366	0.0533	-0.1307	0.0822	-0.0274	0.0248	-0.0502	0.6322	-0.1716	0.0677	0.2686	0.1134	0.5963	29.0566	-18.5174	14.3007
11	0.04	0.0495	-0.0237	0.0625	-0.0293	0.0135	-0.0119	-0.0522	0.0115	-0.1063	-0.051	0.0024	-0.028	-0.0384	-0.06	0.727	0.3446	-0.3325	0.6356	-0.0958	0.7085	3.5631	-24.7366	5.5593
12	0.2152	0.013	-0.0208	0.0028	0.0063	0.0288	-0.1019	0.0331	-0.0568	-0.055	0.0225	0.0106	-0.0163	-0.0258	-0.0059	1.1961	0.0333	-0.1069	0.2866	0.002	0.6561	12.0204	-18.2752	-2.6887
13	0.0997	0.0455	0.0012	0.0957	-0.0174	0.0049	-0.119	-0.0183	-0.1336	-0.2323	0.1661	0.0685	0.1798	-0.1392	0.0607	0.9214	-0.045	-0.0983	0.378	0.2188	0.416	14.9915	-31.2571	-20.4151
14	0.0813	0.0215	-0.0004	0.0109	0.0013	-0.0002	-0.0713	0.0482	0.11	-0.016	0.0082	-0.0012	-0.0279	-0.0146	-0.1476	0.5412	-0.3289	-0.195	0.2374	0.0516	0.211	10.2003	-29.4443	-26.766
15	0.0843	-0.0616	-0.0291	0.1014	0.0762	0.0643	0.0059	-0.0172	0.0353	-0.025	0.0377	-0.0316	0.0076	0.0468	0.0133	0.7289	-0.0607	0.1586	0.2225	-0.0819	0.2364	26.1412	-24.2543	-24.4518
16	0.1138	-0.0979	-0.146	0.1875	0.0532	0.2366	0.1443	0.0101	0.1517	-0.0717	0.0706	-0.0019	-0.0981	-0.0407	0.2834	0.6632	-0.227	-0.0777	0.2215	0.1598	0.7166	11.6464	-19.0045	-20.6427
17	0.1326	-0.1317	-0.159	0.13	0.1572	0.1922	-0.0921	-0.0285	-0.0143	0.1132	0.0262	0.0797	-0.0648	-0.1195	-0.0971	0.6586	-0.0724	-0.2666	0.6482	0.2945	0.6498	-2.9654	-26.0478	-19.8771
18	0.0088	-0.0066	0.0017	0.0184	-0.015	0.0096	0.0138	-0.0959	-0.1572	-0.0167	-0.0357	-0.0568	0.0937	0.049	-0.0001	0.5706	-0.1147	-0.0122	0.2946	0.0119	0.5468	23.3528	-52.7439	32.8478
19	0.0035	-0.0008	0.0001	0.1972	0.0112	0.0192	0.0119	-0.058	-0.0088	0.0584	0.0998	0.2311	0.0938	-0.1547	0.3699	0.0521	-0.3752	0.0858	0.4178	0.1176	0.221	18.0925	-48.0528	40.3295
20	0.1061	-0.0622	0.0457	0.0642	-0.0031	0.0419	0.0573	0.0258	-0.0915	0.0068	0.0098	-0.035	0.0408	-0.0223	0.0595	0.2882	-0.1948	-0.1457	0.4853	0.0548	0.2622	33.5165	-42.0323	42.4694
21	0.1361	0.1275	0.0041	0.1561	0.0259	0.0127	-0.0473	0.0793	0.0626	-0.065	0.0601	-0.0914	-0.0743	0.1033	0.0839	0.3806	-0.2929	-0.1728	0.4969	0.0574	0.2861	36.1246	-26.0796	39.5675
22	0.0215	0.0017	0.0281	0.0277	0.0055	0.0372	-0.1493	0.0036	0.2021	0.2291	-0.0735	0.1673	-0.3279	0.1425	-0.0035	0.4612	-0.081	-0.0063	0.2694	0.0311	0.3044	25.9512	-23.125	36.6667
23	0.084	-0.0102	-0.0211	0.1131	-0.101	0.1007	-0.059	0.0933	-0.0073	0.0845	-0.0121	0.0394	0.0613	-0.0253	-0.4395	0.1828	-0.0376	0.0992	0.4388	-0.0602	0.0557	11.8409	-35.2345	39.8047
24	0.1879	0.0516	-0.0048	0.0481	0.0188	0.012	0.1437	0.0926	0.2	0.0873	-0.0598	0.1679	-0.0923	-0.231	-0.0881	0.6317	0.0764	0.2809	1.0544	0.174	0.486	1.1229	-34.5724	45.3466
25	0.003	0.0091	-0.004	0.0206	-0.0117	0.007	-0.0307	0.0364	-0.1577	-0.0586	0.1459	0.0447	0.0014	-0.0025	0.1096	0.1927	-0.0515	-0.0146	0.8526	-0.0362	0.3049	3.2775	-39.1216	30.4425
26	0.0035	-0.0028	0.0018	0.0049	-0.0006	0.0003	-0.0433	-0.0226	-0.0105	-0.0349	-0.036	0.0026	-0.0409	-0.0354	0.0001	0.6309	0.2092	0.0939	0.5541	-0.2126	0.7735	12.0195	-26.6828	56.0836
27	0.0104	0.0063	0.0289	0.0097	0.0072	0.0993	0.0111	0.0042	-0.0167	0.019	-0.0282	0.0332	-0.0204	0.0255	-0.1731	0.2683	0.0816	0.225	0.5349	-0.0526	0.3231	7.8784	-25.7433	31.8676
28	0.0276	0.0222	0.0205	0.0846	0.0263	0.0171	-0.0159	-0.0236	0.0721	0.0453	-0.08	-0.0203	-0.0194	0.0222	-0.1177	0.8961	-0.1727	0.0551	0.2373	0.0808	0.7678	30.6561	-11.9806	40.0139
29	0.0028	-0.0034	0.004	0.0033	-0.0055	0.0177	-0.0294	-0.0101	-0.0595	-0.0723	-0.0107	-0.0226	-0.0166	-0.0046	0.0001	1.071	0.164	-0.0794	0.7529	-0.0927	0.7168	20.6919	-12.2465	48.8036
30	0.005	-0.0047	-0.0029	0.0058	0.0041	0.0025	0.1441	-0.2063	-0.3526	-0.3539	0.1835	-0.1626	-0.1611	0.0323	0.0001	0.6049	-0.1578	0.0059	0.9686	-0.036	0.6765	24.7066	-24.2544	67.1207
31	0.046	-0.0415	0.0186	0.0416	0.0132	0.1495	-0.0483	-0.0319	0.0937	0.0193	-0.0367	0.077	-0.0571	-0.0113	-0.3768	0.2044	-0.2193	-0.115	0.3906	-0.1489	0.3466	25.3069	-19.2607	73.4458
32	0.0023	0.0002	0.0003	0.0048	-0.0017	0.0021	-0.0302	0.0287	-0.1045	-0.1711	0.0203	0.1335	0.144	-0.0831	0.0002	0.5388	0.1117	-0.0755	0.5519	-0.2043	0.6184	12.0647	-29.9005	70.112
33	0.0062	0.0016	-0.0065	0.0309	-0.008	0.0115	-0.0676	0.0042	0.1033	0.0191	0.1001	-0.0076	-0.0141	0.0073	0.0128	0.5534	-0.0592	-0.345	0.6124	-0.1105	0.7816	16.406	-14.3602	66.1594
34	0.0254	-0.0095	-0.0082	0.005	0.0028	0.0028	0.0317	-0.054	-0.0104	0.1169	-0.0326	-0.056	0.032	0.0084	-0.104	1.119	-0.07	-0.1693	0.5127	-0.3657	0.7098	31.543	-6.3255	69.4569

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(chain A and resid 1:21)
2	X-RAY DIFFRACTION	2	(chain A and (resid 22:45 or resid 60:82))
3	X-RAY DIFFRACTION	3	(chain A and resid 46:59)
4	X-RAY DIFFRACTION	4	(chain A and resid 83:100)
5	X-RAY DIFFRACTION	5	(chain A and (resid 101:112 or resid 234:238 or resid 262:283))
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