PDB-6pqh: Crystal structure of Asparagine-tRNA ligase from Elizabethkingia ...

ID or keywords:

Entry

Database: PDB / ID: 6pqh

Title

Crystal structure of Asparagine-tRNA ligase from Elizabethkingia sp. CCUG 26117

Components

Asparagine--tRNA ligase

Keywords

LIGASE / SSGCID /

Structural Genomics / Elizabethkingia sp. CCUG 26117 / Asparagine--tRNA ligase / Seattle Structural Genomics Center for Infectious Disease

Function / homology

Function and homology information

asparagine-tRNA ligase /

asparagine-tRNA ligase activity / asparaginyl-tRNA aminoacylation /

ATP binding /

cytoplasm
Similarity search - Function

Biological species

Elizabethkingia sp. (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2 Å

Authors

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Citation

Journal: TO BE PUBLISHED
Title: Crystal structure of Asparagine-tRNA ligase from Elizabethkingia sp. CCUG 26117
Authors: Abendroth, J. / Lorimer, D.D. / Horanyi, P.S. / Edwards, T.E.

History

Deposition	Jul 9, 2019	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jul 31, 2019	Provider: repository / Type: Initial release
Revision 1.1	Mar 13, 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
Revision 1.2	Apr 3, 2024	Group: Refinement description / Category: pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6pqh.cif.gz	786 KB	Display	PDBx/mmCIF format
PDB format	pdb6pqh.ent.gz	648.2 KB	Display	PDB format
PDBx/mmJSON format	6pqh.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/pq/6pqh ftp://data.pdbj.org/pub/pdb/validation_reports/pq/6pqh	HTTPS FTP

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Related structure data

Similar structure data	2okx-1 4i0w-d 6dx0-d 5aor-2 4q15-d 3ilv-2 6iv9-d 2q8i-1 3crk-d 1y8p-1 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search
Other databases	TargetTrack: ElmeA.00825.a

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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: Asparagine--tRNA ligase

B: Asparagine--tRNA ligase

C: Asparagine--tRNA ligase

D: Asparagine--tRNA ligase

hetero molecules

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

1

A: Asparagine--tRNA ligase

B: Asparagine--tRNA ligase

hetero molecules

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

2

C: Asparagine--tRNA ligase

D: Asparagine--tRNA ligase

hetero molecules

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

Unit cell

Length a, b, c (Å)	67.400, 110.750, 137.180
Angle α, β, γ (deg.)	90.000, 97.090, 90.000
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Asparagine--tRNA ligase / Asparaginyl-tRNA synthetase / AsnRS Mass: 56703.141 Da / Num. of mol.: 4 / Fragment: ElmeA.00825.a.B1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Elizabethkingia sp. (bacteria) / Gene: asnS / Plasmid: ElmeA.00825.a.B1 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) Strain (production host): BL21(DE3) / References: UniProt: X5KA67, asparagine-tRNA ligase
#2: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂H₆O₂
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 1203 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	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: 2.24 Å³/Da / Density % sol: 45.2 %
Crystal grow	Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: Rigaku Reagents JCSG+ screen, condition a9: 200mM ammonium chloride, 20% (w/V) PEG 3350: ElmeA.00825.a.B1.PW38356 at 24.45mg/ml: grown at 14C: cryo: 20% EG: tray 295595 a9: puck ipi5-9.

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 21-ID-F / Wavelength: 0.97872 Å

Detector

Type: RAYONIX MX-300 / Detector: CCD / Date: Jun 28, 2018

Radiation

Monochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.97872 Å / Relative weight: 1

Reflection

Resolution: 2→35.567 Å / Num. obs: 134701 / % possible obs: 99.9 % / Redundancy: 4.232 % / B_iso Wilson estimate: 35.12 Å² / CC_1/2: 0.999 / R_merge(I) obs: 0.062 / R_rim(I) all: 0.071 / Χ²: 1.037 / Net I/σ(I): 14.98 / Num. measured all: 570031 / Scaling rejects: 78

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. measured obs	Num. possible	Num. unique obs	CC_1/2	R_rim(I) all	% possible all
2-2.05	4.236	0.575	2.55	42456	10035	10023	0.846	0.659	99.9
2.05-2.11	4.244	0.476	3.12	40746	9611	9600	0.89	0.547	99.9
2.11-2.17	4.244	0.381	3.87	40089	9445	9445	0.938	0.437	100
2.17-2.24	4.248	0.315	4.68	38742	9131	9121	0.952	0.362	99.9
2.24-2.31	4.25	0.253	5.75	37685	8871	8867	0.971	0.29	100
2.31-2.39	4.259	0.213	6.82	36506	8587	8572	0.979	0.245	99.8
2.39-2.48	4.252	0.168	8.47	35278	8302	8297	0.987	0.193	99.9
2.48-2.58	4.26	0.147	9.55	33864	7961	7950	0.99	0.168	99.9
2.58-2.7	4.248	0.122	11.15	32622	7688	7680	0.993	0.14	99.9
2.7-2.83	4.253	0.1	13.56	30908	7281	7268	0.995	0.114	99.8
2.83-2.98	4.235	0.074	16.78	29384	6947	6938	0.997	0.085	99.9
2.98-3.16	4.235	0.06	20.14	27967	6614	6603	0.998	0.069	99.8
3.16-3.38	4.233	0.046	24.43	26294	6220	6212	0.999	0.053	99.9
3.38-3.65	4.217	0.036	29.96	24268	5758	5755	0.999	0.041	99.9
3.65-4	4.199	0.029	33.93	22357	5333	5324	0.999	0.033	99.8
4-4.47	4.198	0.024	39.43	20246	4822	4823	1	0.028	100
4.47-5.16	4.21	0.022	41.75	17897	4256	4251	1	0.026	99.9
5.16-6.32	4.189	0.024	39.45	15067	3600	3597	1	0.027	99.9
6.32-8.94	4.124	0.021	40.99	11631	2821	2820	1	0.024	100
8.94-35.567	3.874	0.018	41.42	6024	1587	1555	0.999	0.021	98

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Processing

Software

Name	Version	Classification
XDS		data reduction
XSCALE		data scaling
PHENIX	dev_3500	refinement
PDB_EXTRACT	3.25	data extraction
PHASER		phasing
PHENIX		model building
Coot		model building
BUCCANEER		model building
MR-Rosetta		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: MR-Rosetta model

Resolution: 2→35.567 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.93

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2307	2071	1.54 %	0
R_work	0.1807	-	-	-
obs	0.1814	134461	99.74 %	-

Solvent computation

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

Displacement parameters

B_iso max: 107.74 Å² / B_iso mean: 37.6761 Å² / B_iso min: 13.86 Å²

Refinement step

Cycle: final / Resolution: 2→35.567 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	15180	0	8	1205	16393
B_iso mean	-	-	42.34	41.03	-
Num. residues	-	-	-	-	1899

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / R_factor R_free error: 0

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	% reflection obs (%)
2-2.0465	0.336	138	0.2554	8845	100
2.0465-2.0977	0.2639	145	0.2377	8791	100
2.0977-2.1544	0.2589	147	0.2173	8761	100
2.1544-2.2178	0.2445	140	0.2102	8789	100
2.2178-2.2894	0.2321	143	0.1991	8803	100
2.2894-2.3712	0.2755	124	0.1884	8835	100
2.3712-2.4661	0.2441	138	0.1893	8829	100
2.4661-2.5783	0.2559	133	0.1905	8828	100
2.5783-2.7142	0.2272	147	0.1902	8806	100
2.7142-2.8842	0.244	129	0.1879	8811	100
2.8842-3.1068	0.239	148	0.1883	8837	100
3.1068-3.4192	0.2278	155	0.1818	8826	100
3.4192-3.9134	0.2106	146	0.1621	8857	100
3.9134-4.9284	0.2194	115	0.1434	8910	100
4.9284-35.56	0.1845	123	0.174	8862	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	2.6837	0.2525	0.7512	1.8246	0.0276	4.0085	-0.1206	0.2955	-0.0912	-0.3744	0.0567	-0.0669	0.1758	-0.0107	0.0436	0.2949	0.027	0.0462	0.1644	0.0086	0.1929	-12.4856	-26.6584	-83.7545
2	0.4236	0.0713	-0.2277	0.9902	0.1285	0.754	0.0341	-0.2083	-0.089	0.1203	-0.0402	-0.1472	-0.0117	0.2667	-0.0233	0.1706	0.0056	-0.006	0.3124	0.0818	0.1849	-11.0142	-12.7355	-46.7692
3	0.5341	0.1709	-0.1689	0.9797	-0.0735	0.7924	-0.0186	-0.1578	-0.122	0.1857	-0.0141	0.0272	0.1211	0.1261	0.0223	0.2083	0.0415	0.006	0.2291	0.0858	0.1902	-22.9974	-26.112	-42.7178
4	3.4427	-0.7751	-0.8438	3.1186	0.0921	2.796	-0.0231	-0.4545	-0.0363	0.2817	0.1788	0.4927	-0.2396	-0.5645	-0.1078	0.2721	0.0633	0.0462	0.3644	0.0862	0.3098	-11.8746	4.833	30.2704
5	0.8929	-0.3636	-0.0867	1.4248	0.2061	1.0783	0.041	-0.0709	0.0089	-0.1548	-0.0248	-0.0478	-0.1196	0.0924	-0.0011	0.2143	-0.0502	-0.04	0.1563	0.0023	0.1888	15.1495	-4.4724	9.4128
6	0.4367	-0.4147	-0.0836	2.0402	-0.1558	0.6248	0.1572	-0.0923	0.338	-0.1845	-0.1265	-0.4621	-0.3559	0.2634	-0.054	0.4376	-0.102	0.0781	0.2836	-0.0007	0.4192	27.9244	7.7238	-6.6515
7	0.4874	-0.7356	-0.3114	1.0191	0.2241	1.3194	0.038	-0.067	0.0152	-0.1867	-0.0413	-0.0914	-0.0654	0.1618	-0.0416	0.2087	-0.0592	-0.0119	0.1953	0.0003	0.2619	23.6725	-7.9107	3.1661
8	2.4871	0.1505	0.881	1.487	0.1445	3.4903	0.0444	0.3003	-0.1314	-0.1853	-0.0257	0.0719	0.1529	-0.0728	-0.0439	0.4055	0.0085	-0.0768	0.1973	-0.0171	0.2782	12.7862	-28.5886	-16.0372
9	0.9902	-0.0966	0.0445	1.5322	0.245	1.0775	-0.0167	-0.1913	-0.179	0.0608	0.0351	0.0132	0.0957	0.071	-0.0382	0.2201	-0.0232	-0.0476	0.2297	0.0663	0.2177	14.226	-14.8141	20.968
10	0.5633	-0.7288	-0.4296	1.4123	0.2383	0.8333	-0.2029	-0.2942	-0.4082	0.1559	0.1581	0.5115	0.2766	0.0045	0.0358	0.3305	-0.0191	-0.0121	0.3623	0.1796	0.5027	2.0877	-27.8996	24.6091
11	3.6793	-0.4099	-0.3518	2.6245	0.1485	3.5345	0.1265	-0.2362	0.1678	0.2566	0.1069	0.399	-0.3578	-0.4057	-0.1759	0.2783	0.017	0.1261	0.2487	0.0424	0.298	-37.4657	6.7025	-37.3667
12	0.7437	-0.0424	-0.1641	1.1203	-0.049	1.0843	0.0838	-0.1198	0.0469	0.0181	-0.0673	-0.1329	-0.1514	0.2282	-0.0087	0.1644	-0.0334	0.0051	0.2218	0.034	0.1698	-10.2929	-2.5249	-58.5206
13	1.4853	-0.2398	-0.371	2.2775	-0.4581	1.1994	0.1469	-0.1718	0.3976	0.1056	-0.1477	-0.4655	-0.3505	0.3892	-0.0564	0.3422	-0.0967	0.0697	0.3481	0.0099	0.364	2.2859	9.4494	-74.6387
14	0.3943	-0.1574	-0.4293	0.8167	0.1172	1.3906	0.0919	-0.1376	-0.0035	-0.0408	-0.0601	-0.2048	-0.0819	0.3153	-0.0307	0.1652	-0.0276	0.0153	0.2945	0.0396	0.274	-1.6972	-5.9754	-64.7157

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	chain 'B' and (resid -1 through 129 )	B	-1 - 129
2	X-RAY DIFFRACTION	2	chain 'B' and (resid 130 through 256 )	B	130 - 256
3	X-RAY DIFFRACTION	3	chain 'B' and (resid 257 through 482 )	B	257 - 482
4	X-RAY DIFFRACTION	4	chain 'C' and (resid 2 through 115 )	C	2 - 115
5	X-RAY DIFFRACTION	5	chain 'C' and (resid 116 through 319 )	C	116 - 319
6	X-RAY DIFFRACTION	6	chain 'C' and (resid 320 through 394 )	C	320 - 394
7	X-RAY DIFFRACTION	7	chain 'C' and (resid 395 through 482 )	C	395 - 482
8	X-RAY DIFFRACTION	8	chain 'D' and (resid 1 through 129 )	D	1 - 129
9	X-RAY DIFFRACTION	9	chain 'D' and (resid 130 through 256 )	D	130 - 256
10	X-RAY DIFFRACTION	10	chain 'D' and (resid 257 through 482 )	D	257 - 482
11	X-RAY DIFFRACTION	11	chain 'A' and (resid 1 through 115 )	A	1 - 115
12	X-RAY DIFFRACTION	12	chain 'A' and (resid 116 through 319 )	A	116 - 319
13	X-RAY DIFFRACTION	13	chain 'A' and (resid 320 through 394 )	A	320 - 394
14	X-RAY DIFFRACTION	14	chain 'A' and (resid 395 through 482 )	A	395 - 482

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