PDB-5yyn: Crystal structures of E.coli arginyl-trna synthetase (argrs) in c...

ID or keywords:

Entry

Database: PDB / ID: 5yyn

Title

Crystal structures of E.coli arginyl-trna synthetase (argrs) in complex with substrate TRNA(Arg)

Components

Arginine--tRNA ligase
TRNA

Keywords

LIGASE/RNA / BACTERIAL AMINOACYL-TRNA SYNTHETASES / TRNA ARGINYLATION / DEGENERATED CLASS I SIGNATURE SEQUENCES / TRNA(ARG) IDENTITY ELEMENTS / CONFORMATIONAL ADAPTATION / LIGASE-RNA COMPLEX

Function / homology

Function and homology information

arginine-tRNA ligase / arginine-tRNA ligase activity / arginyl-tRNA aminoacylation / ATP binding / cytosol
Similarity search - Function

Biological species

Escherichia coli (E. coli)

Geobacillus stearothermophilus (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 3 Å

Authors

Zhou, M. / Ye, S. / Stephen, P. / Zhang, R.G. / Wang, E.D. / Giege, R. / Lin, S.X.

Citation

Journal: To Be Published
Title: Crystal Structures Of E.Coli Arginyl-Trna Synthetase (Argrs) In Complex With Substrates
Authors: Zhou, M. / Ye, S. / Stephen, P. / Zhang, R.G. / Wang, E.D. / Giege, R. / Lin, S.X.

History

Deposition	Dec 10, 2017	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Dec 12, 2018	Provider: repository / Type: Initial release
Revision 1.1	Nov 22, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5yyn.cif.gz	600.7 KB	Display	PDBx/mmCIF format
PDB format	pdb5yyn.ent.gz	492.3 KB	Display	PDB format
PDBx/mmJSON format	5yyn.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	5yyn_validation.pdf.gz	485.8 KB	Display	wwPDB validaton report
Full document	5yyn_full_validation.pdf.gz	508.8 KB	Display
Data in XML	5yyn_validation.xml.gz	43.2 KB	Display
Data in CIF	5yyn_validation.cif.gz	60 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/yy/5yyn ftp://data.pdbj.org/pub/pdb/validation_reports/yy/5yyn	HTTPS FTP

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Related structure data

Related structure data	5yymC 1bs2S 4qtv PDB Unreleased entry S: Starting model for refinement C: citing same article (ref.)
Similar structure data	5b63-2 3fs7-d 2xgt-d 5b63-3 5tqh-1 5af4-d 2rf4-d 6eab-d 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

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#121 - Jan 2010 70S Ribosomes similarity (1) #16 - Apr 2001 Aminoacyl-tRNA Synthetases similarity (4) #130 - Oct 2010 Riboswitches similarity (1) #157 - Jan 2013 Transfer-Messenger RNA similarity (1) #181 - Jan 2015 Cascade and CRISPR similarity (1) #229 - Jan 2019 Fluorescent RNA Aptamers similarity (1) #253 - Jan 2021 Expressome similarity (1) #260 - Aug 2021 Ribonuclease P similarity (1) #146 - Feb 2012 Aminoglycoside Antibiotics similarity (1) #15 - Mar 2001 Transfer RNA similarity (1) #249 - Sep 2020 SARS-CoV-2 RNA-dependent RNA Polymerase similarity (1) #10 - Oct 2000 Ribosome similarity (1) #210 - Jun 2017 Adenine Riboswitch in Action similarity (1) #87 - Mar 2007 Zinc Fingers similarity (1) #105 - Sep 2008 Ribonuclease A similarity (1) #226 - Oct 2018 Aminoglycoside Antibiotics and Resistance similarity (1) #245 - May 2020 Spliceosomes similarity (1) #262 - Oct 2021 Fifty Years of Open Access to PDB Structures similarity (1) #65 - May 2005 Self-splicing RNA similarity (1) #98 - Feb 2008 Small Interfering RNA similarity (1) #104 - Aug 2008 Selenocysteine Synthase similarity (1) #106 - Oct 2008 Poly(A) Polymerase similarity (1) #143 - Nov 2011 Toll-like Receptors similarity (1) #161 - May 2013 Ricin similarity (1) #227 - Nov 2018 Telomerase similarity (1) #230 - Feb 2019 Initiation Factor eIF4E similarity (1) #266 - Feb 2022 Oligosaccharyltransferase similarity (1) #81 - Sep 2006 Elongation Factors similarity (1) #89 - May 2007 Aconitase and Iron Regulatory Protein 1 similarity (1) #241 - Jan 2020 Twenty Years of Molecules similarity (1)

PDB pages

PDBj /

wwPDB /

NCBI

Related items in Molecule of the Month

#121 - Jan 2010
70S Ribosomes
similarity (1)
#16 - Apr 2001
Aminoacyl-tRNA Synthetases
similarity (4)
#130 - Oct 2010
Riboswitches
similarity (1)
#157 - Jan 2013
Transfer-Messenger RNA
similarity (1)
#181 - Jan 2015
Cascade and CRISPR
similarity (1)
#229 - Jan 2019
Fluorescent RNA Aptamers
similarity (1)
#253 - Jan 2021
Expressome
similarity (1)
#260 - Aug 2021
Ribonuclease P
similarity (1)
#146 - Feb 2012
Aminoglycoside Antibiotics
similarity (1)
#15 - Mar 2001
Transfer RNA
similarity (1)
#249 - Sep 2020
SARS-CoV-2 RNA-dependent RNA Polymerase
similarity (1)
#10 - Oct 2000
Ribosome
similarity (1)
#210 - Jun 2017
Adenine Riboswitch in Action
similarity (1)
#87 - Mar 2007
Zinc Fingers
similarity (1)
#105 - Sep 2008
Ribonuclease A
similarity (1)
#226 - Oct 2018
Aminoglycoside Antibiotics and Resistance
similarity (1)
#245 - May 2020
Spliceosomes
similarity (1)
#262 - Oct 2021
Fifty Years of Open Access to PDB Structures
similarity (1)
#65 - May 2005
Self-splicing RNA
similarity (1)
#98 - Feb 2008
Small Interfering RNA
similarity (1)
#104 - Aug 2008
Selenocysteine Synthase
similarity (1)
#106 - Oct 2008
Poly(A) Polymerase
similarity (1)
#143 - Nov 2011
Toll-like Receptors
similarity (1)
#161 - May 2013
Ricin
similarity (1)
#227 - Nov 2018
Telomerase
similarity (1)
#230 - Feb 2019
Initiation Factor eIF4E
similarity (1)
#266 - Feb 2022
Oligosaccharyltransferase
similarity (1)
#81 - Sep 2006
Elongation Factors
similarity (1)
#89 - May 2007
Aconitase and Iron Regulatory Protein 1
similarity (1)
#241 - Jan 2020
Twenty Years of Molecules
similarity (1)

Deposited unit

A: Arginine--tRNA ligase

B: TRNA

C: Arginine--tRNA ligase

D: TRNA

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

1

A: Arginine--tRNA ligase

B: TRNA

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

2

C: Arginine--tRNA ligase

D: TRNA

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

Unit cell

Length a, b, c (Å)	102.241, 102.241, 480.567
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	170
Space group name H-M	P6₅

#1: Protein	Arginine--tRNA ligase / Arginyl-tRNA synthetase / ArgRS Mass: 65775.859 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (strain K12) (bacteria) Strain: K12 / Gene: argS, b1876, JW1865 / Production host: Escherichia coli (E. coli) / References: UniProt: P11875, arginine-tRNA ligase
#2: RNA chain	TRNA Mass: 24823.754 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Geobacillus stearothermophilus (bacteria) Production host: Escherichia coli (E. coli) / References: GenBank: 1241824586
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 32 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 4 Å³/Da / Density % sol: 69.26 %
Crystal grow	Temperature: 290 K / Method: vapor diffusion / pH: 5.6 Details: 0.1M NA3C6H5O7, 1.95M (NH4)2SO4, PH 5.6, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 290K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.03988 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 14, 2005
Radiation	Monochromator: SAGITALLY FOCUSED SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.03988 Å / Relative weight: 1
Reflection	Resolution: 3→50 Å / Num. obs: 53802 / % possible obs: 95.4 % / Observed criterion σ(I): 3 / Redundancy: 10.5 % / Net I/σ(I): 13.2
Reflection shell	Resolution: 3→3.1 Å / Redundancy: 7.9 % / R_merge(I) obs: 0.456 / Mean I/σ(I) obs: 2.9 / % possible all: 71.2

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Processing

Software

Name	Version	Classification
HKL-2000		data reduction
HKL-2000		data scaling
PHASER		phasing
PHENIX	1.8.2_1309	refinement

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1BS2

1bs2

Resolution: 3→33.15 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.38

	R_factor	Num. reflection	% reflection
R_free	0.268	2722	5.06 %
R_work	0.22	-	-
obs	0.223	53802	95.3 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 3→33.15 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	8773	2718	0	32	11523

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.003	11966
X-RAY DIFFRACTION	f_angle_d	0.672	16800
X-RAY DIFFRACTION	f_dihedral_angle_d	15.993	4843
X-RAY DIFFRACTION	f_chiral_restr	0.043	1984
X-RAY DIFFRACTION	f_plane_restr	0.003	1700

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 (%)
3-3.0546	0.4288	119	0.3648	1865	X-RAY DIFFRACTION	68
3.0546-3.1133	0.3806	111	0.3463	2307	X-RAY DIFFRACTION	80
3.1133-3.1768	0.4068	149	0.3344	2619	X-RAY DIFFRACTION	94
3.1768-3.2458	0.3411	143	0.3035	2737	X-RAY DIFFRACTION	98
3.2458-3.3212	0.3106	151	0.2721	2840	X-RAY DIFFRACTION	100
3.3212-3.4042	0.3324	142	0.2795	2834	X-RAY DIFFRACTION	99
3.4042-3.4961	0.3027	164	0.2611	2760	X-RAY DIFFRACTION	100
3.4961-3.5989	0.3389	179	0.2587	2786	X-RAY DIFFRACTION	100
3.5989-3.7149	0.2725	149	0.2427	2796	X-RAY DIFFRACTION	100
3.7149-3.8475	0.2657	133	0.2234	2848	X-RAY DIFFRACTION	100
3.8475-4.0013	0.2709	125	0.2156	2846	X-RAY DIFFRACTION	100
4.0013-4.1831	0.2781	170	0.2102	2786	X-RAY DIFFRACTION	100
4.1831-4.4031	0.2583	156	0.1948	2810	X-RAY DIFFRACTION	100
4.4031-4.6783	0.2062	151	0.1733	2830	X-RAY DIFFRACTION	100
4.6783-5.0384	0.2199	136	0.1773	2811	X-RAY DIFFRACTION	99
5.0384-5.5433	0.24	156	0.2025	2788	X-RAY DIFFRACTION	99
5.5433-6.3405	0.262	143	0.2161	2844	X-RAY DIFFRACTION	100
6.3405-7.97	0.2118	141	0.2055	2753	X-RAY DIFFRACTION	97
7.97-33.1483	0.2757	104	0.212	2220	X-RAY DIFFRACTION	78

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	1.0269	0.6013	0.2895	1.5577	0.7478	1.7064	0.0735	0.0429	-0.0493	-0.4297	-0.109	-0.2674	-0.2828	0.3054	-0.7373	0.5775	0.1263	0.1728	0.7087	0.0269	0.6329	62.4201	6.4694	41.4644
2	1.0113	-0.2443	0.5762	1.2374	0.4762	0.6353	-0.053	0.1204	-0.038	-0.2736	0.1477	-0.2759	-0.1896	0.5223	0.0651	0.5183	-0.0997	0.2146	1.0567	0.0643	0.6786	76.6129	17.2144	46.9673
3	-0.0513	0.4036	0.1006	-0.2321	0.0187	0.0665	0.2233	-0.3308	0.1569	0.1188	-0.3022	0.0681	-0.0594	-0.0707	0	0.5082	0.0747	0.1166	0.9185	-0.1116	0.6887	47.6112	18.5134	61.519
4	0.4971	0.5942	-0.1278	0.9069	0.3556	0.9098	0.038	-0.0082	0.0746	-0.0461	-0.1512	0.1886	0.0389	0.0199	-0.0102	0.338	0.1629	0.1458	0.769	-0.0135	0.5718	44.1904	-4.0957	48.0305
5	-0.1876	0.4317	0.2973	0.1895	-0.3092	0.408	-0.0602	0.1743	0.1387	-0.3982	-0.1567	-0.0561	-0.3513	-0.0059	0.0001	0.9371	0.1918	0.0078	1.0075	-0.0215	0.773	50.7864	19.3337	32.3081
6	-0.0882	-0.1374	0.0074	0.0314	0.0044	-0.0217	0.8759	0.0622	0.1318	-0.0252	-0.012	0.3294	0.4139	0.3737	-0.0001	0.9335	0.0625	0.0977	1.6108	-0.1636	0.8994	34.9088	13.7228	41.4585
7	-0.0057	-0.1537	-0.0962	0.0816	0.1004	0.0531	0.3718	0.502	-0.1696	-0.427	0.1666	-0.0867	0.0384	-0.4045	0	1.3314	-0.0712	-0.1616	1.8276	0.1421	1.6245	29.0731	15.1719	34.5412
8	0.4347	-0.4277	-0.1118	-0.0809	-0.7193	0.0783	-0.1247	0.184	0.0997	0.0306	-0.2669	-0.1754	-0.0951	0.2655	0.0002	1.1387	0.3002	-0.0754	1.1392	0.1901	0.7102	55.6562	27.2905	26.6796
9	0.602	-0.2757	0.1142	1.2048	-0.3281	0.7683	0.1051	-0.0535	-0.0562	0.2593	-0.093	0.2075	-0.1626	-0.1109	-0.6335	0.4708	-0.1634	0.1839	0.5732	0.0157	0.4208	42.8042	1.384	103.2375
10	0.1123	0.1667	0.6272	0.876	-0.9926	0.8291	0.1127	0.1377	0.0018	0.118	0.072	0.2563	-0.3343	-0.7283	-0.2749	0.509	0.2058	0.2276	1.1063	-0.056	0.5946	23.9283	18.7619	88.8214
11	0.2425	-0.3426	0.1366	0.7255	-0.3843	0.7913	0.0627	0.0729	0.067	0.0887	-0.2465	-0.1212	-0.0733	0.188	-0.1208	0.3499	-0.1646	0.1349	0.7413	0.0044	0.5454	56.6552	0.3421	89.7051
12	0.3719	1.0072	0.5227	0.8247	0.1256	0.1649	-0.1343	-0.1232	0.2192	0.3796	-0.2486	0.0089	-0.2686	0.0882	0.0001	0.9292	-0.1699	0.0227	1.1109	-0.0557	0.8142	51.4544	19.3208	107.4351
13	-0.0905	0.0864	-0.0038	0.0747	0.0303	-0.035	1.1448	0.0581	0.1084	0.1987	0.5408	-0.0776	-0.058	-0.3481	-0.0001	0.9276	-0.0236	0.1254	1.5739	0.0362	0.9494	67.4001	13.651	98.3377
14	0.0012	0.0057	-0.0363	0.0275	-0.0256	0.0181	-0.2065	-0.1027	0.0059	-0.0191	0.2675	-0.1031	0.1768	0.237	-0	2.4742	0.1774	-0.682	2.6187	-0.0639	2.604	77.0404	7.271	97.75
15	0.7281	1.0431	0.6701	0.2032	1.2136	0.4351	-0.0525	-0.1494	0.0639	0.2509	-0.1351	0.1449	-0.2581	-0.0344	0	1.1109	-0.2757	-0.0203	1.1562	-0.1315	0.788	49.5626	26.28	112.5894

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(CHAIN A AND RESID 1:221 )
2	X-RAY DIFFRACTION	2	(CHAIN A AND RESID 222:373 )
3	X-RAY DIFFRACTION	3	(CHAIN A AND RESID 374:408 )
4	X-RAY DIFFRACTION	4	(CHAIN A AND RESID 409:577 )
5	X-RAY DIFFRACTION	5	(CHAIN B AND RESID 901:922 )
6	X-RAY DIFFRACTION	6	(CHAIN B AND RESID 923:928 )
7	X-RAY DIFFRACTION	7	(CHAIN B AND RESID 929:948 )
8	X-RAY DIFFRACTION	8	(CHAIN B AND RESID 949:975 )
9	X-RAY DIFFRACTION	9	(CHAIN C AND RESID 1:183 )
10	X-RAY DIFFRACTION	10	(CHAIN C AND RESID 184:362 )
11	X-RAY DIFFRACTION	11	(CHAIN C AND RESID 363:577 )
12	X-RAY DIFFRACTION	12	(CHAIN D AND RESID 901:922 )
13	X-RAY DIFFRACTION	13	(CHAIN D AND RESID 923:928 )
14	X-RAY DIFFRACTION	14	(CHAIN D AND RESID 940:944 )
15	X-RAY DIFFRACTION	15	(CHAIN D AND RESID 945:975 )

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