PDB-8ie2: Crystal structure of Lactiplantibacillus plantarum GlyRS

ID or keywords:

Entry

Database: PDB / ID: 8ie2

Title

Crystal structure of Lactiplantibacillus plantarum GlyRS

Components

Glycine--tRNA ligase alpha subunit
Glycine--tRNA ligase beta subunit

Keywords

TRANSFERASE / LIGASE / aminoacyl-tRNA synthetase

Function / homology

Function and homology information

glycyl-tRNA aminoacylation / glycine-tRNA ligase / glycine-tRNA ligase activity / transferase activity / ATP binding / cytoplasm
Similarity search - Function

Biological species

Lactiplantibacillus plantarum WCFS1 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 3.6 Å

Authors

Yamashita, S. / Tomita, K.

Funding support

Japan, 2items

Citation

Journal: J.Biochem. / Year: 2023
Title: Mechanism of tRNA recognition by heterotetrameric glycyl-tRNA synthetase from lactic acid bacteria.
Authors: Nagato, Y. / Yamashita, S. / Ohashi, A. / Furukawa, H. / Takai, K. / Tomita, K. / Tomikawa, C.

History

Deposition	Feb 15, 2023	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Jun 7, 2023	Provider: repository / Type: Initial release
Revision 1.1	Jun 14, 2023	Group: Database references / Category: citation Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2	Sep 13, 2023	Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / citation Item: _citation.journal_volume / _citation.page_first / _citation.page_last

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8ie2.cif.gz	1.4 MB	Display	PDBx/mmCIF format
PDB format	pdb8ie2.ent.gz	1.2 MB	Display	PDB format
PDBx/mmJSON format	8ie2.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8ie2_validation.pdf.gz	511.7 KB	Display	wwPDB validaton report
Full document	8ie2_full_validation.pdf.gz	599.2 KB	Display
Data in XML	8ie2_validation.xml.gz	132.9 KB	Display
Data in CIF	8ie2_validation.cif.gz	179.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ie/8ie2 ftp://data.pdbj.org/pub/pdb/validation_reports/ie/8ie2	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	#16 - Apr 2001 Aminoacyl-tRNA Synthetases similarity (2)

Deposited unit

B: Glycine--tRNA ligase alpha subunit

A: Glycine--tRNA ligase alpha subunit

D: Glycine--tRNA ligase alpha subunit

C: Glycine--tRNA ligase alpha subunit

H: Glycine--tRNA ligase beta subunit

F: Glycine--tRNA ligase beta subunit

E: Glycine--tRNA ligase beta subunit

G: Glycine--tRNA ligase beta subunit

453 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

B: Glycine--tRNA ligase alpha subunit

A: Glycine--tRNA ligase alpha subunit

F: Glycine--tRNA ligase beta subunit

E: Glycine--tRNA ligase beta subunit

defined by author
Evidence: gel filtration
227 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

D: Glycine--tRNA ligase alpha subunit

C: Glycine--tRNA ligase alpha subunit

H: Glycine--tRNA ligase beta subunit

G: Glycine--tRNA ligase beta subunit

defined by author
227 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	155.140, 163.170, 155.280
Angle α, β, γ (deg.)	90.00, 119.81, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Glycine--tRNA ligase alpha subunit / Glycyl-tRNA synthetase alpha subunit / GlyRS Mass: 34729.066 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: The N-terminal GlyPro is derived from expression vector. (Rest of the HRV3c cleavage site) Source: (gene. exp.) Lactiplantibacillus plantarum WCFS1 (bacteria) Strain: WCFS1 / Gene: glyQ / Production host: Escherichia coli (E. coli) / References: UniProt: Q88VS2, glycine-tRNA ligase
#2: Protein	Glycine--tRNA ligase beta subunit / Glycyl-tRNA synthetase beta subunit / GlyRS Mass: 78633.539 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lactiplantibacillus plantarum WCFS1 (bacteria) Strain: WCFS1 / Gene: glyS / Production host: Escherichia coli (E. coli) / References: UniProt: Q88VS3, glycine-tRNA ligase

#1: Protein

Glycine--tRNA ligase alpha subunit / Glycyl-tRNA synthetase alpha subunit / GlyRS

Mass: 34729.066 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: The N-terminal GlyPro is derived from expression vector. (Rest of the HRV3c cleavage site)
Source: (gene. exp.)

Lactiplantibacillus plantarum WCFS1 (bacteria)
Strain: WCFS1 / Gene: glyQ / Production host:

Escherichia coli (E. coli) / References: UniProt: Q88VS2, glycine-tRNA ligase

#2: Protein

Glycine--tRNA ligase beta subunit / Glycyl-tRNA synthetase beta subunit / GlyRS

Mass: 78633.539 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Lactiplantibacillus plantarum WCFS1 (bacteria)
Strain: WCFS1 / Gene: glyS / Production host:

Escherichia coli (E. coli) / References: UniProt: Q88VS3, glycine-tRNA ligase

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 3.77 Å³/Da / Density % sol: 67.34 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 12% PEG3350, 4% Tacsimate pH 5.0

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

Photon Factory

/ Beamline: BL-17A / Wavelength: 0.98 Å

Detector

Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 30, 2019

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.98 Å / Relative weight: 1

Reflection

Resolution: 3.6→50 Å / Num. obs: 46387 / % possible obs: 59.5 % / Redundancy: 6.8 % / CC_1/2: 0.989 / R_merge(I) obs: 0.258 / R_rim(I) all: 0.279 / Net I/σ(I): 6.82

Reflection shell

Resolution (Å)	R_merge(I) obs	Num. unique obs	CC_1/2	R_rim(I) all	Diffraction-ID
3.6-3.69	0.678	691	0.746	0.735	1
3.69-3.8	0.688	1180	0.739	0.743	1
3.8-3.91	0.645	1515	0.828	0.697	1
3.91-4.03	0.605	1784	0.851	0.654	1
4.03-4.16	0.56	2031	0.883	0.605	1
4.16-4.3	0.501	2307	0.92	0.541	1
4.3-4.47	0.422	2466	0.94	0.457	1
4.47-4.65	0.393	2667	0.943	0.426	1
4.65-4.85	0.403	2869	0.94	0.437	1
4.85-5.09	0.429	2962	0.93	0.468	1
5.09-5.37	0.465	3176	0.93	0.503	1
5.37-5.69	0.525	3241	0.915	0.564	1
5.69-6.09	0.527	3450	0.917	0.567	1
6.09-6.57	0.454	3334	0.934	0.488	1
6.57-7.2	0.298	3022	0.965	0.32	1
7.2-8.05	0.166	2786	0.989	0.179	1
8.05-9.3	0.099	2435	0.994	0.107	1
9.3-11.39	0.066	2052	0.996	0.073	1
11.39-16.1	0.063	1600	0.997	0.068	1
16.1-50	0.062	819	0.997	0.068	1

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Processing

Software

Name	Version	Classification
PHENIX	1.18.2	refinement
XSCALE		data scaling
XDS		data reduction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 3.6→48.63 Å / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.44 / Stereochemistry target values: TWIN_LSQ_F
Details: The anisotropically scaled and truncated mtz file were used for the final refinement.

	R_factor	Num. reflection	% reflection
R_free	0.2442	2383	5.14 %
R_work	0.2153	-	-
obs	0.2217	46387	59.64 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 3.6→48.63 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	30972	0	0	0	30972

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.004	31608
X-RAY DIFFRACTION	f_angle_d	0.852	42738
X-RAY DIFFRACTION	f_dihedral_angle_d	22.552	11838
X-RAY DIFFRACTION	f_chiral_restr	0.051	4696
X-RAY DIFFRACTION	f_plane_restr	0.006	5576

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 (%)
3.6-3.67	0.324	24	0.2926	436	X-RAY DIFFRACTION	10
3.67-3.75	0.3492	53	0.2779	792	X-RAY DIFFRACTION	17
3.75-3.84	0.2871	56	0.2769	1098	X-RAY DIFFRACTION	24
3.84-3.94	0.2495	56	0.2568	1314	X-RAY DIFFRACTION	29
3.94-4.04	0.2986	62	0.2446	1544	X-RAY DIFFRACTION	34
4.04-4.16	0.2662	94	0.24	1763	X-RAY DIFFRACTION	38
4.16-4.3	0.2988	115	0.2405	2003	X-RAY DIFFRACTION	44
4.3-4.45	0.2636	103	0.2274	2230	X-RAY DIFFRACTION	49
4.45-4.63	0.2308	143	0.2194	2487	X-RAY DIFFRACTION	54
4.63-4.84	0.2608	142	0.2089	2766	X-RAY DIFFRACTION	61
4.84-5.09	0.2751	179	0.2073	3033	X-RAY DIFFRACTION	66
5.09-5.41	0.2563	166	0.2221	3451	X-RAY DIFFRACTION	75
5.41-5.83	0.2946	197	0.2238	3878	X-RAY DIFFRACTION	85
5.83-6.41	0.2588	238	0.2318	4305	X-RAY DIFFRACTION	93
6.42-7.34	0.2303	232	0.2149	4301	X-RAY DIFFRACTION	94
7.34-9.24	0.2135	234	0.1933	4336	X-RAY DIFFRACTION	94
9.24-48.63	0.2105	253	0.211	4303	X-RAY DIFFRACTION	92

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	1.4135	-0.4522	-0.1031	0.8735	0.5602	1.4373	0.2161	0.1528	-0.0845	-0.208	0.0156	-0.1469	0.4178	0.0333	-0.208	0.4785	-0.0257	0.0026	0.3994	-0.0808	0.2574	2.707	-3.451	33.279
2	1.8442	-0.3938	-0.3065	0.629	-0.6257	1.6163	0.2149	0.1539	-0.1319	-0.0635	0.0102	-0.0819	0.1857	0.1806	-0.2074	0.2473	-0.0522	-0.1024	0.2083	-0.0932	0.2583	8.708	0.286	55.439
3	1.6944	0.2443	0.1553	1.3101	0.2674	1.8067	-0.1197	0.1454	0.2395	0.1641	0.1131	-0.3998	-0.0287	-0.0631	-0.004	0.3759	-0.0638	-0.1498	0.2753	-0.0166	0.4715	-4.738	-66.413	57.582
4	1.2241	0.3267	-0.1033	1.5425	-0.1728	1.8171	-0.0323	0.0371	0.1831	-0.0729	-0.1107	-0.1739	-0.0035	-0.0167	0.1235	0.0814	0.0055	0.0117	0.3524	0.0771	0.4079	-20.921	-70.039	41.273
5	0.6368	0.0016	-0.663	-0.0001	0.0509	2.9788	0.2299	-0.3721	-0.3591	-0.7322	0.3089	0.5077	0.862	0.4618	-0.5191	0.709	-0.0826	-0.3244	0.63	-0.1565	0.9125	-25.394	-5.867	9.96
6	0.2554	-0.4491	-0.5089	1.0298	0.529	1.5345	0.7139	0.619	-0.2062	-0.1288	0.6804	-0.8501	-0.9291	-0.0131	-0.9765	1.1818	-0.0286	-0.2132	0.9331	-0.1251	0.8593	-50.789	-31.975	-16.892
7	1.385	0.2691	0.4701	0.381	0.3679	0.494	0.0219	-0.0731	-0.1963	-0.2944	-0.0116	0.0757	-0.3428	0.0973	-0.0319	0.5333	-0.2186	0.1427	0.4536	0.0886	0.4207	0.489	15.843	7.191
8	2.6005	0.1176	-0.1604	2.0471	0.3131	2.5033	0.0712	-0.1279	-0.7167	0.1009	0.2558	0.2884	0.6888	-0.3966	-0.1685	0.6961	-0.0461	0.2154	0.6575	0.1023	0.5793	22.396	-9.207	-3.684
9	0.8089	0.7931	0.35	0.7691	0.3465	0.15	-0.0034	0.0166	-0.4284	0.1631	0.2296	0.1808	1.3316	-0.6966	-0.1959	1.442	-0.3046	-0.0482	0.758	0.2324	1.2597	14.975	-32.327	-33.322
10	1.3423	-0.5272	0.3163	0.6526	-0.4733	1.2307	-0.0538	0.0836	0.5005	0.3443	-0.2374	0.0888	-0.4888	0.3683	0.1989	0.2837	-0.1908	0.0267	0.3389	-0.1906	0.5143	8.116	24.832	82.819
11	0.9053	0.0553	-0.2385	0.0539	0.0405	0.1225	0.207	-0.1387	-0.233	0.2988	-0.0526	-0.2395	0.1472	-0.0601	-0.0486	1.4237	-0.8374	0.1633	1.2872	-0.2171	0.6557	19.882	40.555	91.766
12	1.7254	-0.3546	1.2396	1.3123	-0.8187	1.7888	0.1494	0.292	-0.587	-0.2872	0.2268	0.066	0.385	0.0133	0.0494	-0.008	-0.2374	0.0408	0.5157	-0.0117	0.2542	-5.585	-5.921	83.728
13	2.1446	0.3317	-0.5496	1.9467	-0.7798	1.6404	0.3219	-0.4043	-0.7677	0.2543	-0.2694	-0.6768	-0.0757	0.3263	-0.0366	0.6334	0.1452	-0.2735	0.4907	-0.1481	0.827	24.876	-21.48	86.63
14	1.1825	0.1988	0.7053	0.741	-0.451	0.8511	0.243	0.1814	-0.2815	-0.4978	-0.0497	-0.0379	-0.256	0.2669	-0.125	0.7961	-0.168	-0.0059	0.5216	-0.2486	0.8015	49.075	-11.392	114.52
15	0.8633	0.9777	0.6541	2.463	1.1961	0.6474	-0.0845	-0.8411	0.0987	0.3862	-0.4562	0.2384	-0.1086	-1.0117	0.5835	0.8268	0.0129	-0.1508	0.9916	-0.1903	0.7658	1.357	-63.764	93.701
16	0.2518	0.0512	0.1539	0.6594	-0.3671	0.8505	0.0984	-0.0236	-0.1651	0.2849	0.0645	-0.1957	0.391	0.1877	-0.2098	1.4762	0.4663	-0.5818	0.7017	-0.2942	0.825	3.046	-49.733	110.519
17	0.4411	0.2817	-0.4978	0.3736	0.05	1.4111	-0.1033	-0.2969	-0.067	0.2372	-0.3046	-0.1041	0.5186	0.093	0.2695	0.428	-0.0124	-0.1391	0.49	0.1859	0.6149	16.683	-85.285	72.319
18	1.9595	0.677	-0.2128	2.2677	0.2163	1.2476	0.0726	-0.2659	0.8984	-0.0244	-0.0824	0.4772	-0.4173	-0.139	-0.0942	0.2257	0.0383	0.1279	0.4483	0.1611	0.6293	37.419	-60.304	59.171
19	0.2615	-0.0797	0.3352	0.8824	-1.4078	2.4621	0.1027	0.1944	-0.1212	0.7961	-0.2153	-0.0847	-0.2965	0.3778	-0.0456	0.8701	0.1956	0.1013	0.4943	-0.2113	0.8821	59.68	-38.039	80.983
20	2.1019	-0.3457	-0.016	1.6348	-0.8551	2.7803	-0.1413	0.2086	-0.4253	-0.064	0.4536	-0.0409	0.5713	0.1967	-0.1665	0.2291	-0.0452	0.0574	0.4278	-0.1411	0.3991	-44.979	-94.655	28.321
21	0.393	0.0188	-0.1188	0.0429	0.1619	0.6628	0.5496	-0.1539	-0.3568	-0.1048	-0.2631	0.3735	0.9564	0.0883	-0.3816	1.8259	-0.2082	-0.3975	0.6151	-0.033	1.3914	-43.764	-123.95	-2.33
22	0.7542	-0.2117	-0.4203	1.6648	0.2111	1.5482	0.0528	-0.0653	0.2	-0.0539	-0.0976	-0.0734	-0.3015	0.0367	-0.0388	0.0179	0.021	0.0491	0.2916	0.0714	0.1854	-52.52	-63.799	39.853
23	1.7273	-0.2036	0.1871	0.3908	-0.2959	1.7042	0.1451	0.4193	0.0286	-0.02	-0.1104	-0.17	0.1306	0.2281	-0.0439	0.4352	0.046	0.0778	0.3179	0.0158	0.3824	-40.901	-48.363	11.744
24	0.29	-0.2574	-0.1412	0.6695	-0.7257	1.6533	0.1922	0.2838	-0.0719	-0.2503	0.0502	0.4022	0.7608	-0.0502	-0.1571	0.9513	-0.1052	-0.1474	0.556	-0.0476	0.6795	-52.693	-58.901	-22.441

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	( CHAIN A AND RESID 1:299 )	A	1 - 299
2	X-RAY DIFFRACTION	2	( CHAIN B AND RESID 1:299 )	B	1 - 299
3	X-RAY DIFFRACTION	3	( CHAIN C AND RESID 1:299 )	C	1 - 299
4	X-RAY DIFFRACTION	4	( CHAIN D AND RESID 1:299 )	D	1 - 299
5	X-RAY DIFFRACTION	5	( CHAIN E AND ( RESID 1:63 OR RESID 125:212 ) )	E	1 - 63
6	X-RAY DIFFRACTION	5	( CHAIN E AND ( RESID 1:63 OR RESID 125:212 ) )	E	125 - 212
7	X-RAY DIFFRACTION	6	( CHAIN E AND RESID 64:124 )	E	64 - 124
8	X-RAY DIFFRACTION	7	( CHAIN E AND RESID 213:337 )	E	213 - 337
9	X-RAY DIFFRACTION	8	( CHAIN E AND RESID 338:545 )	E	338 - 545
10	X-RAY DIFFRACTION	9	( CHAIN E AND RESID 546:694 )	E	546 - 694
11	X-RAY DIFFRACTION	10	( CHAIN F AND ( RESID 1:63 OR RESID 125:212 ) )	F	1 - 63
12	X-RAY DIFFRACTION	10	( CHAIN F AND ( RESID 1:63 OR RESID 125:212 ) )	F	125 - 212
13	X-RAY DIFFRACTION	11	( CHAIN F AND RESID 64:124 )	F	64 - 124
14	X-RAY DIFFRACTION	12	( CHAIN F AND RESID 213:337 )	F	213 - 337
15	X-RAY DIFFRACTION	13	( CHAIN F AND RESID 338:545 )	F	338 - 545
16	X-RAY DIFFRACTION	14	( CHAIN F AND RESID 546:694 )	F	546 - 694
17	X-RAY DIFFRACTION	15	( CHAIN G AND ( RESID 1:63 OR RESID 125:212 ) )	G	1 - 63
18	X-RAY DIFFRACTION	15	( CHAIN G AND ( RESID 1:63 OR RESID 125:212 ) )	G	125 - 212
19	X-RAY DIFFRACTION	16	( CHAIN G AND RESID 64:124 )	G	64 - 124
20	X-RAY DIFFRACTION	17	( CHAIN G AND RESID 213:337 )	G	213 - 337
21	X-RAY DIFFRACTION	18	( CHAIN G AND RESID 338:545 )	G	338 - 545
22	X-RAY DIFFRACTION	19	( CHAIN G AND RESID 546:694 )	G	546 - 694
23	X-RAY DIFFRACTION	20	( CHAIN H AND ( RESID 1:63 OR RESID 125:212 ) )	H	1 - 63
24	X-RAY DIFFRACTION	20	( CHAIN H AND ( RESID 1:63 OR RESID 125:212 ) )	H	125 - 212
25	X-RAY DIFFRACTION	21	( CHAIN H AND RESID 64:124 )	H	64 - 124
26	X-RAY DIFFRACTION	22	( CHAIN H AND RESID 213:337 )	H	213 - 337
27	X-RAY DIFFRACTION	23	( CHAIN H AND RESID 338:545 )	H	338 - 545
28	X-RAY DIFFRACTION	24	( CHAIN H AND RESID 546:694 )	H	546 - 694

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