PDB-8i9i: Glutamyl-tRNA synthetase from Escherichia Coli bound to Glutamate...

ID or keywords:

Entry

Database: PDB / ID: 8i9i

Title

Glutamyl-tRNA synthetase from Escherichia Coli bound to Glutamate and Zinc

Components

Glutamate--tRNA ligase

Keywords

LIGASE

Function / homology

Function and homology information

glutamate-tRNA ligase /

glutamate-tRNA ligase activity / glutamyl-tRNA aminoacylation /

tRNA binding / zinc ion binding /

ATP binding /

cytosol
Similarity search - Function

Biological species

Escherichia coli (E. coli)

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT / Resolution: 3.3 Å

Authors

Dev, A. / Chongdar, N. / Dasgupta, S. / Basu, G.

Funding support

India, 1items

Citation

Journal: To Be Published
Title: Escherichia coli GluRS
Authors: Dev, A. / Chongdar, N. / Dasgupta, S. / Basu, G.

History

Deposition	Feb 7, 2023	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Apr 19, 2023	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8i9i.cif.gz	384.7 KB	Display	PDBx/mmCIF format
PDB format	pdb8i9i.ent.gz	321.1 KB	Display	PDB format
PDBx/mmJSON format	8i9i.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/i9/8i9i ftp://data.pdbj.org/pub/pdb/validation_reports/i9/8i9i	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 (5) #235 - Jul 2019 AMPA Receptor similarity (1) #191 - Nov 2015 Glutamate-gated Chloride Receptors similarity (1)

Deposited unit

A: Glutamate--tRNA ligase

B: Glutamate--tRNA ligase

hetero molecules

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

1

Idetical with deposited unit
defined by author
Evidence: gel filtration, monomer

Unit cell

Length a, b, c (Å)	211.510, 61.290, 101.900
Angle α, β, γ (deg.)	90.00, 96.69, 90.00
Int Tables number	5
Space group name H-M	C121

#1: Protein	Glutamate--tRNA ligase / Glutamyl-tRNA synthetase Mass: 53462.176 Da / Num. of mol.: 2 / Mutation: K236E, E328A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: gltX / Production host: Escherichia coli (E. coli) / References: UniProt: P04805, glutamate-tRNA ligase
#2: Chemical	ChemComp-GLU / GLUTAMIC ACID / Glutamic acid Type: L-peptide linking / Mass: 147.129 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₅H₉NO₄ / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 169 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 3.07 Å³/Da / Density % sol: 59.99 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.1M MOPS HEPESNa pH 7.7, 0.02M l-glu, 14% PEG 8000, 22% ehylene glycol PH range: 7.3-7.9

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Data collection

Diffraction	Mean temperature: 110 K / Serial crystal experiment: N
Diffraction source	Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5419 Å
Detector	Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Oct 6, 2011
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.5419 Å / Relative weight: 1
Reflection	Resolution: 3.3→43.65 Å / Num. obs: 19872 / % possible obs: 99.79 % / Redundancy: 2 % / CC_1/2: 0.98 / Net I/σ(I): 8.78
Reflection shell	Resolution: 3.3→3.41 Å / Num. unique obs: 1968 / CC_1/2: 0.294

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Processing

Software

Name	Version	Classification
PHENIX	1.15.2_3472	refinement
PDB_EXTRACT	3.25	data extraction
MOSFLM		data reduction
SCALA		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 3.3→43.644 Å / SU ML: 0.56 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 31.15 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2963	1004	5.06 %
R_work	0.2532	-	-
obs	0.2554	19858	99.85 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 3.3→43.644 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7322	0	22	169	7513

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.002	7515
X-RAY DIFFRACTION	f_angle_d	0.415	10207
X-RAY DIFFRACTION	f_dihedral_angle_d	1.815	4480
X-RAY DIFFRACTION	f_chiral_restr	0.037	1105
X-RAY DIFFRACTION	f_plane_restr	0.003	1353

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 (%)
3.3001-3.474	0.3401	140	0.3251	2659	X-RAY DIFFRACTION	100
3.474-3.6915	0.3131	162	0.2964	2660	X-RAY DIFFRACTION	100
3.6915-3.9764	0.3706	142	0.2792	2652	X-RAY DIFFRACTION	100
3.9764-4.3762	0.3186	125	0.2681	2720	X-RAY DIFFRACTION	100
4.3762-5.0087	0.2901	152	0.2347	2671	X-RAY DIFFRACTION	100
5.0087-6.3074	0.2976	140	0.2516	2702	X-RAY DIFFRACTION	100
6.3074-43.45	0.2356	143	0.2037	2790	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	4.1044	-2.1186	2.9036	3.3049	-0.539	5.5043	0.0695	-0.5884	-0.2392	-0.403	0.3984	0.3136	0.17	-0.8293	-0.4354	0.5451	-0.0822	0.0319	0.3847	0.0789	0.5651	-7.7817	-6.1307	25.0602
2	4.9802	-2.2417	2.8346	3.6443	-0.5417	4.6141	0.9181	0.0274	-0.7037	-1.5583	-0.3248	0.617	1.0226	-0.2408	-0.5429	0.9265	-0.1203	-0.3238	0.6815	-0.016	0.958	-23.2596	-6.9543	2.094
3	4.9502	-2.2485	2.6258	2.4414	-0.6807	4.3376	0.1748	1.4269	1.0716	-1.5134	-0.7385	-0.4687	-0.9223	0.4289	0.4215	1.7099	-0.1289	-0.1206	0.7904	0.3322	1.1315	-14.4301	11.0943	-7.1171
4	2.5634	-2.3063	0.7966	2.8424	-2.7136	5.3023	0.5747	1.0328	0.2709	-0.5428	-0.383	0.8144	-1.57	-0.937	0.1156	1.6311	0.1193	-0.1727	0.9529	0.2759	0.869	-24.1198	7.7805	-4.4511
5	8.3941	-3.0145	2.0006	4.1173	0.7004	6.7625	0.5164	0.6496	-0.3762	-1.0604	-0.9262	1.0728	-0.6578	-1.3232	-0.2428	1.4237	0.5433	-0.8141	1.2891	-0.1378	1.2839	-32.1501	-6.1936	-11.8255
6	6.3078	-0.9254	-2.2252	1.2265	2.1122	8.293	0.3654	0.6314	-2.0847	-1.0654	-0.392	0.9966	0.8784	-0.831	-0.6139	0.7557	0.0791	-0.1367	0.7744	0.34	1.9216	-24.6275	-12.2678	-8.6249
7	4.0273	0.0478	2.5765	2.7736	2.818	8.3631	-0.2881	0.0853	0.0937	-0.8276	0.16	0.4233	-1.4455	-1.051	0.1542	0.7821	0.1592	-0.0383	0.5289	0.1798	0.7195	-22.4348	5.3097	9.412
8	4.5747	-0.8077	2.6567	3.6811	3.3014	8.6397	0.2816	-0.6596	0.1734	-0.4438	-0.1994	0.2558	0.4023	-1.4876	-0.1688	0.4502	-0.0792	-0.0907	0.6598	0.1338	0.6703	-20.3351	0.5383	17.6321
9	2.2674	0.1578	1.2895	1.6279	-0.9128	2.8816	0.0074	0.7039	1.1392	-1.2078	-0.2012	-0.6761	-0.6382	0.5348	0.6743	1.0773	0.0738	0.3474	0.4697	0.1803	1.0623	4.0435	11.1316	20.167
10	4.0114	-1.769	1.2225	1.8064	0.0572	3.5361	0.2074	0.0758	0.3221	-1.3084	-0.2952	-0.5226	0.1688	0.2959	0.243	0.521	-0.0306	0.1114	0.3	-0.0439	0.656	7.5386	-1.3523	30.982
11	1.3136	-1.2624	1.1344	2.8384	0.0562	1.7635	-0.366	-0.9817	1.6897	0.6929	0.1926	-0.23	-1.6768	-1.3277	0.4286	0.8322	0.3221	-0.096	0.6655	-0.2587	1.0198	-3.0112	10.1026	38.2899
12	5.4008	-2.0325	1.9985	3.4603	-0.8321	3.7397	-0.4343	-1.4489	0.5597	0.816	0.1872	0.056	-0.8594	-1.6728	0.2674	0.9562	-0.217	0.0991	0.8931	-0.0257	0.5631	-7.8321	1.6	42.431
13	2.1576	-0.5636	1.9148	2.9616	-0.8307	5.2207	-1.0703	-0.3121	0.9048	0.1871	-0.4207	-1.1301	-1.1336	-0.8363	-0.3389	0.8112	0.1904	-0.1109	0.1029	-0.292	1.2092	0.8927	10.0373	34.4993
14	4.5825	-1.4258	1.8978	1.6818	-1.0364	2.9986	-0.2531	-0.5519	0.1526	0.0164	0.404	-0.7347	-0.0878	-0.3477	0.1815	0.5425	0.0214	0.0533	0.1849	0.0634	0.6869	15.1243	-9.1408	43.0314
15	3.3529	-1.2461	1.0753	3.0685	-0.4426	1.831	-0.4072	-0.4036	0.5453	0.2672	0.0957	-1.2961	-0.2221	0.1425	0.2201	0.386	0.0404	-0.0594	0.24	0.032	1.1954	25.1632	-5.3778	41.4493
16	3.1134	-0.0291	1.9246	0.2019	-0.4193	1.8518	-0.2569	-0.0675	0.2061	0.6021	0.1575	-1.0585	-0.23	1.0142	0.6402	0.2202	0.0794	-1.7055	1.2169	-0.3297	1.9994	44.9308	-2.0049	50.1755
17	2.5534	-0.9173	1.0537	1.3165	-1.9857	3.0589	-0.5335	-1.2424	-0.2458	0.7611	0.0906	-0.5902	-0.2165	0.2513	0.1809	1.5912	0.6969	-0.8336	1.1011	-0.0213	1.5286	37.6284	-10.8087	61.4787
18	3.955	0.3196	1.4958	0.6817	-0.0063	1.9031	-0.7609	-2.0286	0.5134	1.3661	0.0003	-0.3741	-0.7463	0.1296	0.4372	1.3357	0.497	-0.559	1.6048	-0.2282	1.4395	34.057	-2.7451	61.9667
19	3.0684	-0.8939	-2.8721	1.5521	0.566	2.8777	-1.3975	-1.0842	0.318	0.3577	0.6068	-0.5219	0.1507	0.3814	-0.0777	0.6983	0.1443	-0.4359	0.6997	0.0851	1.2088	34.5663	-7.6236	50.5458
20	4.2226	-2.0139	-2.7727	1.9521	1.2794	1.8373	-0.2975	-0.8938	0.5827	0.8486	0.9157	-1.0483	0.593	2.5283	1.095	0.963	-0.2847	0.0508	-0.7818	0.7062	1.1288	39.7865	-6.1773	39.2555
21	2.857	0.2487	0.8099	2.8369	-0.173	3.8954	-0.1221	-0.87	0.3287	0.3333	0.4729	-0.9451	-0.3615	0.1376	0.115	0.6191	0.1377	-0.2801	0.6424	-0.2369	0.7696	23.2988	26.6231	69.5667
22	3.1296	0.7025	1.3376	2.3322	-0.4546	3.0712	-0.2441	-0.9175	0.5899	0.4717	0.1992	-0.5454	-0.2224	0.1521	0.1629	0.5783	0.0984	-0.1612	0.6103	-0.2223	0.8072	23.0492	29.9141	65.0547
23	1.2897	0.9361	1.2305	2.1847	-0.7028	2.5424	0.2681	-0.4872	-0.1594	0.2953	-0.654	-1.0163	0.1642	0.2989	-0.039	1.1253	0.0647	-0.6736	1.5154	-0.1869	1.3269	44.3694	24.2876	85.9977
24	1.0239	0.6819	-0.5051	5.52	0.9532	0.5765	0.4578	-2.4096	-1.7708	1.1869	0.6986	-0.2785	0.875	0.1347	-0.8223	1.644	0.3184	-0.5009	2.2807	0.6156	1.8729	48.2777	24.2295	98.4526
25	0.4452	0.6797	0.1404	1.3617	1.1064	2.3421	0.4884	-1.274	-0.1554	0.1821	0.1646	-0.8342	-0.2	0.4211	0.7199	0.9532	-0.3107	-1.5188	1.5319	0.0155	1.4468	49.2634	31.7335	90.4471
26	1.6277	0.3522	-0.9277	0.1691	-0.2478	0.5503	0.0023	-1.3091	-0.4623	0.585	-0.6142	-0.7428	-0.0714	-0.0249	0.4483	1.207	0.1142	-0.5674	1.8309	-0.0257	1.0899	37.0777	17.4992	90.1428
27	0.196	0.7908	-0.2443	2.7378	-1.1251	1.0252	0.2683	-1.6424	-0.0752	-0.1244	-0.3462	-0.5795	0.166	-0.041	0.4542	0.8204	-0.0736	-0.3917	1.3589	0.0619	1.2371	34.23	16.076	81.7363
28	0.5828	0.3171	-0.5293	0.6957	-0.1837	0.5036	-0.0323	-1.358	-0.0337	0.287	0.0322	-0.2916	-0.2486	-0.369	0.3078	1.2229	0.307	-0.7523	1.4342	-0.0453	0.777	33.8873	26.4001	78.3549
29	1.3474	1.69	-1.3114	2.7425	-0.9936	2.2932	-0.7416	-1.6178	0.0175	0.3199	-0.395	-0.4602	-0.3798	0.0985	-0.6846	0.6892	0.206	-0.4742	1.5531	-0.3137	0.6232	27.3212	21.3132	78.9334
30	0.5724	0.6044	-0.1207	2.5505	-0.9978	0.4203	0.0873	-0.9448	-0.045	0.5512	-0.4443	-0.4175	-0.2394	-0.2945	0.0856	0.7161	-0.3162	-0.3533	1.825	-0.3179	1.1715	23.5661	22.3914	87.1106
31	2.5796	0.0859	-0.0823	2.715	-0.0262	4.8409	-0.4835	-0.6776	-0.302	0.0966	0.1678	-1.8944	0.6207	0.7643	0.1554	0.5449	0.1375	-0.0596	0.5184	0.0387	0.9876	25.1446	19.2559	54.4962
32	3.2159	-0.7774	-0.1429	2.8826	-0.2552	4.0932	-0.7235	-0.8426	-1.308	-0.0438	0.0345	-0.4865	1.8576	-0.2905	-0.0451	0.9839	-0.1411	-0.0922	0.8774	0.2401	0.7292	11.9975	10.594	57.5869
33	3.933	-0.9168	0.0814	2.7528	-0.9627	5.6294	-0.4967	-0.5601	-0.1565	-0.5528	0.4933	-0.4914	1.1152	-0.1779	-0.0013	0.6777	-0.0656	-0.0702	0.3159	-0.045	0.6224	13.4946	16.3522	54.3605
34	1.7635	-0.3954	-0.0064	1.55	0.2043	2.3186	0.143	-0.428	0.2348	-1.0208	0.2537	-0.9254	-0.6352	-0.4582	0.209	0.6294	-0.0136	-0.0034	-0.1299	-0.0438	0.6773	12.7522	35.3251	38.568
35	2.101	0.037	0.3508	3.6319	-0.9354	2.8792	-0.2689	0.2802	-0.2306	-1.0518	0.4869	-0.5527	0.8992	-0.1162	0.137	0.9897	-0.0806	0.2417	0.3123	0.03	0.5147	15.8394	29.9741	29.8093
36	0.8512	0.2754	-0.3523	1.4619	0.0043	4.1044	-0.2514	0.6412	-0.339	-1.1495	-0.1938	-0.7366	0.781	0.333	0.1356	1.5173	0.1479	1.1388	1.2637	0.0165	1.6409	20.2286	24.0825	13.8667
37	1.197	-1.0044	0.5974	1.1961	-0.8528	0.6528	-0.3382	0.6069	-0.1147	-1.4101	0.0835	-0.1774	0.556	-0.0867	0.0114	2.2499	-0.3973	0.4143	1.0951	-0.1745	0.3495	12.6015	24.6089	6.8277
38	1.1681	0.4514	-0.8511	0.1904	-0.1602	3.3176	-0.1942	0.6513	0.3499	-1.7146	0.4464	0.7919	0.0117	-0.9537	0.0562	1.7379	-0.2323	-0.1693	0.605	0.0388	0.6239	-1.6489	32.8823	15.791
39	2.7449	-0.2814	-1.068	1.5196	-1.1309	1.8846	0.016	1.0067	-0.832	-1.5204	0.503	0.5004	1.3412	-0.7832	0.1579	1.9139	-0.2993	0.1086	0.4947	0.1535	0.7405	5.4184	24.7136	15.4033
40	1.3197	-0.0266	0.0747	1.9428	-0.255	2.2229	-0.3945	0.5114	0.1729	-1.2612	0.4053	-0.8024	0.0062	-0.0714	-0.0155	1.3842	-0.1445	0.1943	0.5084	0.0759	0.5934	11.1573	34.5914	17.3944

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(chain A and resid 1:75)
2	X-RAY DIFFRACTION	2	(chain A and resid 76:108)
3	X-RAY DIFFRACTION	3	(chain A and resid 109:113)
4	X-RAY DIFFRACTION	4	(chain A and resid 114:128)
5	X-RAY DIFFRACTION	5	(chain A and resid 129:133)
6	X-RAY DIFFRACTION	6	(chain A and resid 134:139)
7	X-RAY DIFFRACTION	7	(chain A and resid 140:180)
8	X-RAY DIFFRACTION	8	(chain A and resid 181:226)
9	X-RAY DIFFRACTION	9	(chain A and resid 227:243)
10	X-RAY DIFFRACTION	10	(chain A and resid 244:261)
11	X-RAY DIFFRACTION	11	(chain A and resid 262:278)
12	X-RAY DIFFRACTION	12	(chain A and resid 279:284)
13	X-RAY DIFFRACTION	13	(chain A and resid 285:309)
14	X-RAY DIFFRACTION	14	(chain A and resid 310:346)
15	X-RAY DIFFRACTION	15	(chain A and resid 347:371)
16	X-RAY DIFFRACTION	16	(chain A and resid 372:390)
17	X-RAY DIFFRACTION	17	(chain A and resid 391:396)
18	X-RAY DIFFRACTION	18	(chain A and resid 397:427)
19	X-RAY DIFFRACTION	19	(chain A and resid 428:464)
20	X-RAY DIFFRACTION	20	(chain A and resid 465:501)
21	X-RAY DIFFRACTION	21	(chain B and resid 1:14)
22	X-RAY DIFFRACTION	22	(chain B and resid 15:75)
23	X-RAY DIFFRACTION	23	(chain B and resid 76:125)
24	X-RAY DIFFRACTION	24	(chain B and resid 126:131)
25	X-RAY DIFFRACTION	25	(chain B and resid 132:141)
26	X-RAY DIFFRACTION	26	(chain B and resid 142:146)
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30	X-RAY DIFFRACTION	30	(chain B and resid 217:222)
31	X-RAY DIFFRACTION	31	(chain B and resid 223:265)
32	X-RAY DIFFRACTION	32	(chain B and resid 266:275)
33	X-RAY DIFFRACTION	33	(chain B and resid 276:313)
34	X-RAY DIFFRACTION	34	(chain B and resid 314:345)
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36	X-RAY DIFFRACTION	36	(chain B and resid 372:378)
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38	X-RAY DIFFRACTION	38	(chain B and resid 385:410)
39	X-RAY DIFFRACTION	39	(chain B and resid 411:441)
40	X-RAY DIFFRACTION	40	(chain B and resid 442:501)

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