PDB-9ymm: Crystal structure of Glutamate--tRNA ligase (GltX) from Moraxella...

ID or keywords:

Entry

Database: PDB / ID: 9ymm

Title

Crystal structure of Glutamate--tRNA ligase (GltX) from Moraxella catarrhalis in complex with 5'-O-(N-Glutamyl)sulfamoyladeonosine

Components

Glutamate--tRNA ligase

Keywords

LIGASE / SSGCID / STRUCTURAL GENOMICS / SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE / Glutamate--tRNA ligase (GltX)

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

Moraxella catarrhalis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.92 Å

Authors

Seattle Structural Genomics Center for Infectious Disease / Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Funding support

United States, 2items

Organization	Grant number	Country
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	75N93022C00036	United States
National Institutes of Health/Office of the Director	S10OD030394	United States

Citation

Journal: To be published
Title: Crystal structure of Glutamate--tRNA ligase (GltX) from Moraxella catarrhalis in complex with 5'-O-(N-Glutamyl)sulfamoyladeonosine
Authors: Enayati, P. / Liu, L. / Lovell, S. / Battaile, K.P.

History

Deposition	Oct 10, 2025	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 22, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9ymm.cif.gz	765.9 KB	Display	PDBx/mmCIF format
PDB format	pdb9ymm.ent.gz	637.9 KB	Display	PDB format
PDBx/mmJSON format	9ymm.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9ymm_validation.pdf.gz	2.1 MB	Display	wwPDB validaton report
Full document	9ymm_full_validation.pdf.gz	2.2 MB	Display
Data in XML	9ymm_validation.xml.gz	75.2 KB	Display
Data in CIF	9ymm_validation.cif.gz	95.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ym/9ymm ftp://data.pdbj.org/pub/pdb/validation_reports/ym/9ymm	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)

Deposited unit

A: Glutamate--tRNA ligase

B: Glutamate--tRNA ligase

C: Glutamate--tRNA ligase

D: Glutamate--tRNA ligase

hetero molecules

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

1

A: Glutamate--tRNA ligase

B: Glutamate--tRNA ligase

hetero molecules

defined by author
Evidence: gel filtration
121 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: Glutamate--tRNA ligase

D: Glutamate--tRNA ligase

hetero molecules

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

Unit cell

Length a, b, c (Å)	53.713, 124.225, 458.212
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Glutamate--tRNA ligase / Glutamyl-tRNA synthetase / GluRS Mass: 58885.523 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Moraxella catarrhalis (bacteria) / Gene: gltX, AO370_0559 / Plasmid: MocaA.01348.a.UX11 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0AB36DQE3, glutamate-tRNA ligase
#2: Chemical	ChemComp-GSU / O5'-(L-GLUTAMYL-SULFAMOYL)-ADENOSINE Type: L-peptide linking / Mass: 475.434 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₁₅H₂₁N₇O₉S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	... ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 40 / Source method: obtained synthetically / Formula: SO₄
#4: Chemical	ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400 Mass: 282.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₂H₂₆O₇ / Comment: precipitant*YM
#5: Chemical	ChemComp-2PE / NONAETHYLENE GLYCOL Mass: 414.488 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₈H₃₈O₁₀ / Comment: precipitant*YM
Has ligand of interest	Y
Has protein modification	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: 3.25 Å³/Da / Density % sol: 62.1 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5 Details: Grid Salt HT B2: 2.4M ammonium sulfate, 0.1M citrate pH 5.0, MocaA.01348.a.UX11.PS38771 at 26.6 mg/mL. 2mM ligand added prior to crystallization. Plate 20153 B2 drop 1 , Puck: PSL-0805, Cryo: ...Details: Grid Salt HT B2: 2.4M ammonium sulfate, 0.1M citrate pH 5.0, MocaA.01348.a.UX11.PS38771 at 26.6 mg/mL. 2mM ligand added prior to crystallization. Plate 20153 B2 drop 1 , Puck: PSL-0805, Cryo: 2.5 M ammonium sulfate.

Crystal

Density Matthews: 3.25 Å³/Da / Density % sol: 62.1 %

Crystal grow

Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5
Details: Grid Salt HT B2: 2.4M ammonium sulfate, 0.1M citrate pH 5.0, MocaA.01348.a.UX11.PS38771 at 26.6 mg/mL. 2mM ligand added prior to crystallization. Plate 20153 B2 drop 1 , Puck: PSL-0805, Cryo: ...

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: NSLS-II / Beamline: 19-ID / Wavelength: 0.9786 Å
Detector	Type: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Jul 26, 2025
Radiation	Monochromator: Double Crystal Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9786 Å / Relative weight: 1
Reflection	Resolution: 2.92→49.3 Å / Num. obs: 68405 / % possible obs: 100 % / Redundancy: 13.2 % / CC_1/2: 0.997 / R_merge(I) obs: 0.218 / R_pim(I) all: 0.062 / R_rim(I) all: 0.227 / Χ²: 1.11 / Net I/σ(I): 11.4 / Num. measured all: 906211
Reflection shell	Resolution: 2.92→3 Å / % possible obs: 100 % / Redundancy: 13.9 % / R_merge(I) obs: 1.471 / Num. measured all: 70232 / Num. unique obs: 5044 / CC_1/2: 0.851 / R_pim(I) all: 0.406 / R_rim(I) all: 1.526 / Χ²: 0.94 / Net I/σ(I) obs: 1.7

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Processing

Software

Name	Version	Classification
PHENIX	(2.0_5765: ???)	refinement
Aimless		data scaling
XDS		data reduction
PHASER		phasing
PDB_EXTRACT		data extraction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.92→49.3 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.9 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2526	3353	4.92 %
R_work	0.2145	-	-
obs	0.2164	68197	99.81 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.92→49.3 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	14941	0	375	0	15316

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.005	15649
X-RAY DIFFRACTION	f_angle_d	0.776	21275
X-RAY DIFFRACTION	f_dihedral_angle_d	12.794	5684
X-RAY DIFFRACTION	f_chiral_restr	0.044	2316
X-RAY DIFFRACTION	f_plane_restr	0.008	2685

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 (%)
2.92-2.96	0.4015	143	0.3515	2717	X-RAY DIFFRACTION	100
2.96-3.01	0.3999	133	0.3366	2643	X-RAY DIFFRACTION	100
3.01-3.05	0.3877	131	0.3252	2610	X-RAY DIFFRACTION	100
3.05-3.1	0.3962	130	0.3234	2698	X-RAY DIFFRACTION	100
3.1-3.16	0.4208	153	0.3268	2679	X-RAY DIFFRACTION	100
3.16-3.21	0.3698	124	0.3127	2611	X-RAY DIFFRACTION	100
3.21-3.28	0.3512	134	0.2772	2662	X-RAY DIFFRACTION	100
3.28-3.34	0.3304	126	0.2671	2698	X-RAY DIFFRACTION	100
3.34-3.42	0.2757	138	0.2477	2630	X-RAY DIFFRACTION	100
3.42-3.49	0.2732	152	0.2409	2668	X-RAY DIFFRACTION	100
3.49-3.58	0.299	128	0.2422	2712	X-RAY DIFFRACTION	100
3.58-3.68	0.2488	125	0.2371	2611	X-RAY DIFFRACTION	100
3.68-3.79	0.2568	136	0.2265	2693	X-RAY DIFFRACTION	100
3.79-3.91	0.2759	149	0.2099	2690	X-RAY DIFFRACTION	100
3.91-4.05	0.2138	126	0.1857	2674	X-RAY DIFFRACTION	100
4.05-4.21	0.2264	160	0.1797	2705	X-RAY DIFFRACTION	100
4.21-4.4	0.1887	150	0.17	2679	X-RAY DIFFRACTION	100
4.4-4.63	0.1958	138	0.1716	2705	X-RAY DIFFRACTION	100
4.63-4.92	0.1797	121	0.1607	2762	X-RAY DIFFRACTION	100
4.92-5.3	0.2413	146	0.1737	2715	X-RAY DIFFRACTION	100
5.3-5.84	0.2314	146	0.2019	2737	X-RAY DIFFRACTION	100
5.84-6.68	0.2843	142	0.2184	2789	X-RAY DIFFRACTION	100
6.68-8.41	0.2351	154	0.1973	2783	X-RAY DIFFRACTION	100
8.41-49.3	0.2015	168	0.1839	2973	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	2.4769	-1.455	1.0431	0.4792	-0.453	1.6665	-0.1535	0.0125	-0.113	0.0204	0.1345	0.0917	-0.1137	0.1311	-0	0.537	-0.0556	0.0174	0.3153	-0.0897	0.4584	11.7671	46.5496	26.5696
2	1.4165	-0.3497	-0.048	1.9457	0.3601	0.4298	-0.0016	-0.1006	0.4211	0.0125	-0.2637	0.3598	-0.6668	-0.4386	-0.1007	0.5435	0.1171	0.03	0.2955	-0.073	0.6274	0.568	51.6276	19.8752
3	0.6413	-0.5824	-0.5896	0.4396	0.7037	0.5074	0.2706	0.0923	-0.0479	0.0856	-0.8506	0.6543	-0.3953	-0.6202	-0.0242	0.7491	-0.0081	-0.2548	1.0833	-0.2225	0.8379	-2.7473	31.1061	1.1064
4	2.1053	0.7891	0.2636	1.9795	0.0548	1.502	0.0149	1.062	0.1427	-0.4014	-0.1966	0.1819	-0.3635	-0.1811	-0.255	0.6289	0.1226	-0.0309	0.5482	-0.1795	0.6234	1.6625	40.1543	2.4599
5	2.5807	-0.5174	-0.0662	-0.33	0.5973	0.95	0.1492	0.5906	0.0658	-0.1414	-0.1724	0.121	-0.2169	0.1705	-0.0682	0.5173	0.0337	-0.0079	0.2775	-0.0998	0.465	10.9404	42.394	11.6457
6	1.0861	0.6914	-0.4897	0.984	0.2317	0.7089	-0.0987	-0.3006	-0.1261	0.0031	-0.0745	-0.3843	0.2335	1.3747	-0.0104	0.6272	0.0035	0.0018	0.7316	0.0734	0.5496	26.2968	39.9266	34.161
7	2.0323	1.394	1.5151	2.9384	-0.3679	2.6045	-0.7592	-0.523	2.0159	-1.2826	0.308	1.5701	0.1522	-1.2997	-0.6412	0.5015	-0.0191	-0.2075	0.2397	0.3408	0.4534	13.7929	38.4053	56.028
8	0.3259	1.0164	-0.1179	1.0273	0.0871	0.9169	-0.1437	-0.1102	-0.1458	-0.196	0.2735	0.133	0.3447	-0.4253	0.01	0.7727	-0.0969	-0.0944	0.5564	0.1163	0.642	6.5084	18.9413	44.2671
9	1.278	-0.0963	0.095	1.7714	0.1475	0.4583	0.0613	-0.1683	0.4122	0.2087	-0.0203	-0.2695	-0.0412	0.1176	-0	0.5881	-0.012	0.0072	1.0395	0.1341	0.647	24.3955	39.7318	103.8192
10	1.6528	-0.6697	0.6566	1.4738	-0.4545	0.9142	0.253	-0.3278	-0.334	-0.0565	-0.2895	0.4855	0.1424	-0.3604	-0.0206	0.5181	-0.0256	0.0426	0.8912	0.2066	0.534	10.8693	27.8623	88.894
11	0.6725	0.4061	-0.3873	2.6545	-1.4984	0.7678	0.5744	-1.5167	0.5326	0.1379	-0.3531	0.1693	-0.9964	0.4859	0.0419	0.5346	0.0213	-0.1001	0.8261	-0.0822	0.537	18.2479	38.2984	64.8831
12	0.1404	0.009	0.3884	0.1543	-0.2212	0.5276	-0.2031	0.2169	-0.2512	-0.0716	0.3752	-0.233	-0.3944	-0.7544	-0.0049	0.4658	-0.0482	0.0173	0.7799	0.0305	0.5943	28.668	23.8578	60.6665
13	1.1637	0.6879	0.7454	1.3121	0.8256	0.6962	0.016	-0.0993	0.0616	0.0654	0.0513	-0.1079	-0.0845	0.2353	0	0.5272	-0.0052	-0.0144	0.9621	0.2155	0.7566	38.4101	23.7093	74.7695
14	0.7498	0.591	-0.7437	1.4591	-0.8657	0.6457	0.1644	-0.3808	-0.13	-0.0423	-0.134	-0.2569	-0.0074	-0.4123	0.0017	0.5464	-0.0196	-0.0717	0.9686	-0.089	0.5877	-16.1205	69.6286	92.2688
15	0.4117	0.1864	0.0721	2.2333	0.1061	-0.0352	0.1242	-0.0566	-0.0056	0.5618	-0.1167	0.322	0.3873	-0.0954	0	0.8118	-0.1032	0.0841	0.961	-0.0017	0.7624	-26.9596	60.8409	105.1634
16	2.0339	0.4374	0.1174	1.6962	-0.349	0.2761	0.2679	-0.4588	-0.0438	0.7481	-0.3206	-0.2383	-0.1444	0.3171	-0	0.7712	-0.144	-0.0074	1.029	-0.1146	0.5237	-21.1021	73.9406	108.5943
17	0.4363	0.6055	-0.0815	0.2391	0.5522	1.0089	0.1879	-0.7213	0.2933	0.0893	-0.0169	-0.2959	0.0043	0.4587	0.0069	0.5259	-0.0151	-0.0134	0.8134	-0.1315	0.571	-6.096	81.179	82.226
18	1.4789	-1.3677	-1.124	0.5519	0.4529	0.5516	-0.0681	-0.0719	-0.0794	-0.2594	-0.1447	-0.0006	-0.1089	0.0321	0	0.5767	-0.0631	0.0189	0.5746	-0.0049	0.5124	-24.9045	84.757	60.3357
19	2.4404	-0.7072	-0.7365	2.6687	0.102	0.1026	0.0005	-0.398	-0.0566	0.0879	-0.0262	0.1274	0.1227	-0.1918	0	0.4653	0.0108	0.0149	0.6869	-0.1114	0.5302	-35.0602	87.1937	74.7094
20	1.4994	-0.4429	0.3193	-1.0271	-1.3116	2.4204	0.0647	0.4633	0.0076	-0.0286	-0.0881	-0.2663	0.0167	0.1976	-0.0028	0.6264	0.0021	0.021	0.3407	0.0454	0.5535	-3.2203	74.5075	17.9012
21	0.0945	0.5028	0.2254	2.5876	-0.0295	0.1383	0.0186	0.1538	0.7421	0.216	0.2546	-1.5678	-0.0396	0.0864	0.2622	0.7261	0.0767	0.2232	0.9669	0.4269	0.8901	8.0176	90.7614	-2.0251
22	2.2031	-0.1032	-0.0565	0.9976	-0.4334	1.2874	0.0528	0.6114	0.1377	-0.2739	-0.1849	-0.0463	-0.0056	0.1407	-0.0001	0.659	0.007	-0.0232	0.5346	0.1136	0.5604	-9.8435	80.0486	7.9225
23	0.4261	0.6253	-0.3176	0.2548	0.0438	0.7118	-0.0786	0.0004	0.0632	-0.0009	0.0306	0.3116	-0.0724	-0.9835	-0	0.6541	-0.0274	-0.0143	0.6756	-0.0672	0.5798	-23.5475	77.9474	32.3031
24	-0.0216	0.1493	-0.0989	0.8288	1.6147	2.8349	0.2798	0.8908	-1.2554	-1.0056	0.509	-1.7031	0.6538	1.6921	0.784	0.527	0.1893	0.1974	0.0192	-0.5702	0.5227	-10.3594	75.0071	54.0523
25	0.7767	0.5415	0.3246	1.5934	-0.5742	0.6057	-0.1836	-0.0605	0.1279	-0.0919	0.2757	-0.258	-0.1936	0.5416	0.0294	0.7051	-0.1941	0.1002	0.5051	-0.114	0.6302	-3.0824	95.8139	46.3395

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 10 through 79 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 80 through 114 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 115 through 153 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 154 through 185 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 186 through 265 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 266 through 344 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 345 through 370 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 371 through 510 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 15 through 245 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 246 through 344 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 345 through 370 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 371 through 404 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 405 through 511 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 15 through 79 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 80 through 161 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 162 through 265 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 266 through 358 )
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 359 through 404 )
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 405 through 511 )
20	X-RAY DIFFRACTION	20	chain 'D' and (resid 16 through 132 )
21	X-RAY DIFFRACTION	21	chain 'D' and (resid 133 through 170 )
22	X-RAY DIFFRACTION	22	chain 'D' and (resid 171 through 265 )
23	X-RAY DIFFRACTION	23	chain 'D' and (resid 266 through 344 )
24	X-RAY DIFFRACTION	24	chain 'D' and (resid 345 through 370 )
25	X-RAY DIFFRACTION	25	chain 'D' and (resid 371 through 510 )

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+About Yorodumi

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-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

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Movie

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Structure viewers

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Viewer log

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This page

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This web site

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Options

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Open data

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Basic information

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Structure visualization

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Downloads & links

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Download

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Validation report

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Related structure data

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Links

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Assembly

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Components

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Experimental details

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Experiment

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Sample preparation

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Data collection

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Processing

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About Yorodumi

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News

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Feb 9, 2022. New format data for meta-information of EMDB entries

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Aug 12, 2020. Covid-19 info

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Mar 5, 2020. Novel coronavirus structure data

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Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

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Jul 12, 2017. Major update of PDB

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Yorodumi