PDB-9o68: Crystal Structure of Tryptophanyl-tRNA synthetase from Klebsiella...

ID or keywords:

Entry

Database: PDB / ID: 9o68

Title

Crystal Structure of Tryptophanyl-tRNA synthetase from Klebsiella aerogenes (tryptophan bound)

Components

Tryptophan--tRNA ligase

Keywords

LIGASE / SSGCID / STRUCTURAL GENOMICS / SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE / Tryptophanyl-tRNA synthetase / Klebsiella aerogenes

Function / homology

Function and homology information

tryptophan-tRNA ligase / tryptophanyl-tRNA aminoacylation / tryptophan-tRNA ligase activity / ATP binding / cytosol
Similarity search - Function

Biological species

Klebsiella aerogenes KCTC 2190 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.15 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 Tryptophanyl-tRNA synthetase from Klebsiella aerogenes (tryptophan bound)
Authors: Seibold, S. / Lovell, S. / Battaile, K.P.

History

Deposition	Apr 11, 2025	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Apr 23, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	9o68.cif.gz	264.2 KB	Display	PDBx/mmCIF format
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PDBx/mmJSON format	9o68.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/o6/9o68 ftp://data.pdbj.org/pub/pdb/validation_reports/o6/9o68	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) #228 - Dec 2018 Directed Evolution of Enzymes similarity (1)

Deposited unit

A: Tryptophan--tRNA ligase

B: Tryptophan--tRNA ligase

hetero molecules

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

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	49.054, 120.798, 55.830
Angle α, β, γ (deg.)	90.00, 94.87, 90.00
Int Tables number	4
Space group name H-M	P12₁1

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Protein , 1 types, 2 molecules AB

#1: Protein	Tryptophan--tRNA ligase / Tryptophanyl-tRNA synthetase / TrpRS Mass: 39766.152 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Klebsiella aerogenes KCTC 2190 (bacteria) Gene: trpS, EAE_05135 / Plasmid: KlaeA.00241.a.UX1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0H3FKK2, tryptophan-tRNA ligase

#1: Protein

Tryptophan--tRNA ligase / Tryptophanyl-tRNA synthetase / TrpRS

Mass: 39766.152 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Klebsiella aerogenes KCTC 2190 (bacteria)
Gene: trpS, EAE_05135 / Plasmid: KlaeA.00241.a.UX1 / Production host:

Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0H3FKK2, tryptophan-tRNA ligase

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Non-polymers , 5 types, 156 molecules

#2: Chemical	ChemComp-TRP / TRYPTOPHAN Type: L-peptide linking / Mass: 204.225 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₁H₁₂N₂O₂ / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO₄
#5: Chemical	ChemComp-PG4 / TETRAETHYLENE GLYCOL Mass: 194.226 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C₈H₁₈O₅ / Comment: precipitant*YM
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 148 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has ligand of interest	Y
Has protein modification	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: 2.07 Å³/Da / Density % sol: 40.65 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: Berkeley

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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: Dec 15, 2024
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: 2.15→48.88 Å / Num. obs: 34439 / % possible obs: 98 % / Redundancy: 3.5 % / CC_1/2: 0.999 / R_merge(I) obs: 0.058 / R_pim(I) all: 0.037 / R_rim(I) all: 0.069 / Χ²: 0.95 / Net I/σ(I): 12.6 / Num. measured all: 120058
Reflection shell	Resolution: 2.15→2.22 Å / % possible obs: 94.2 % / Redundancy: 3.3 % / R_merge(I) obs: 0.551 / Num. measured all: 9365 / Num. unique obs: 2868 / CC_1/2: 0.769 / R_pim(I) all: 0.353 / R_rim(I) all: 0.657 / Χ²: 1 / Net I/σ(I) obs: 2.2

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Processing

Software

Name	Version	Classification
PHENIX	dev_5660	refinement
Aimless		data scaling
XDS		data reduction
PHASER		phasing
PDB_EXTRACT		data extraction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.15→48.88 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.6 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2225	1710	4.97 %
R_work	0.1799	-	-
obs	0.1821	34400	97.8 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.15→48.88 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4900	0	64	148	5112

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.003	5058
X-RAY DIFFRACTION	f_angle_d	0.566	6860
X-RAY DIFFRACTION	f_dihedral_angle_d	16.518	1832
X-RAY DIFFRACTION	f_chiral_restr	0.041	773
X-RAY DIFFRACTION	f_plane_restr	0.005	891

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 (%)
2.15-2.21	0.2988	131	0.234	2596	X-RAY DIFFRACTION	94
2.21-2.28	0.2485	159	0.2073	2675	X-RAY DIFFRACTION	97
2.28-2.37	0.2376	154	0.198	2710	X-RAY DIFFRACTION	98
2.37-2.46	0.2358	160	0.1949	2747	X-RAY DIFFRACTION	98
2.46-2.57	0.2379	123	0.1825	2726	X-RAY DIFFRACTION	98
2.57-2.71	0.2914	121	0.1857	2757	X-RAY DIFFRACTION	98
2.71-2.88	0.2446	145	0.1922	2742	X-RAY DIFFRACTION	99
2.88-3.1	0.2712	156	0.2092	2749	X-RAY DIFFRACTION	99
3.1-3.41	0.2328	141	0.185	2706	X-RAY DIFFRACTION	98
3.41-3.91	0.2036	136	0.1666	2770	X-RAY DIFFRACTION	99
3.91-4.92	0.1746	137	0.1461	2780	X-RAY DIFFRACTION	99
4.92-48.88	0.215	147	0.1875	2732	X-RAY DIFFRACTION	97

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	1.3996	-0.9795	-0.7219	0.7282	0.24	1.9986	-0.0344	-0.4976	-0.1145	0.168	0.0174	0.1673	-0.0275	-0.1551	0.0272	0.3198	0.0258	-0.0123	0.464	-0.0268	0.3361	1.871	3.871	9.872
2	0.4767	-0.499	-0.1416	1.5459	0.3662	0.7897	0.0063	-0.1246	0.0226	0.2207	0.0231	0.0332	0.0319	0.0152	-0.0376	0.3079	0.025	-0.0063	0.3527	-0.0215	0.2496	8.046	-5.24	4.421
3	4.1332	-0.6243	-1.3971	0.7353	0.618	0.9822	-0.1057	-0.6228	-0.0797	0.2455	0.1637	-0.1443	0.0614	0.4369	-0.2104	0.393	0.048	-0.0847	0.4556	-0.0022	0.3875	8.271	0.124	16.253
4	2.9854	0.0222	-0.3794	2.726	-0.4656	3.0169	-0.1193	-0.0161	-0.255	0.1922	0.1908	-0.0457	0.0818	0.0537	-0.084	0.3503	0.0113	-0.0141	0.3487	0.0121	0.2929	-13.947	6.205	26.05
5	1.1286	-0.1371	-2.8156	0.3826	0.4386	6.9226	0.0525	0.1647	-0.0505	0.0356	-0.2684	0.1304	-0.7731	-0.7847	0.1223	0.3546	0.0884	-0.0167	0.4306	-0.0199	0.3524	-13.912	12.607	11.227
6	2.7644	-1.5832	-0.8174	1.873	0.8627	0.5671	-0.0435	-0.0677	0.3407	-0.1567	0.2018	-0.3888	-0.1354	0.0919	-0.1379	0.3381	-0.046	0.0269	0.3597	0.0034	0.3182	14.723	1.06	-7.701
7	2.003	-0.4773	-1.2859	2.5296	1.0325	1.1974	-0.2133	-0.1429	-0.045	0.2705	0.046	-0.3627	0.3659	-0.0671	0.1485	0.3237	-0.037	0.0224	0.2847	-0.0338	0.4224	22.414	-26.348	-23.616
8	2.1735	-0.382	-0.3876	1.2733	0.0792	1.947	0.0874	0.009	0.0085	-0.1354	0.0352	-0.1839	-0.0853	0.0506	-0.1397	0.2893	0.0253	0.0155	0.2658	-0.0068	0.319	23.689	-19.044	-20.868
9	1.5949	-0.5064	0.2418	0.3915	0.2682	2.0691	0.0252	0.0406	-0.3258	-0.0228	0.0701	0.0317	0.2327	0.0644	-0.0417	0.3227	0.0086	-0.0161	0.3107	0.0049	0.3821	9.806	-22.286	-8.85
10	3.0913	-2.2781	-1.0659	1.6757	0.6211	0.4704	-0.0687	-0.0751	-0.3878	-0.005	0.006	0.1194	0.0721	0.0582	0.0808	0.3393	-0.0359	-0.068	0.3265	-0.0043	0.498	9.938	-30.098	-16.23
11	1.6119	1.0676	0.026	4.5025	-0.8999	2.0431	-0.1397	-0.0206	-0.393	0.3971	0.0944	-1.1034	0.1682	-0.0519	0.0581	0.5134	0.0176	0.024	0.4679	-0.0766	0.667	36.261	-43.948	-25.92
12	0.1551	0.2754	-0.0836	3.826	0.4458	0.7852	-0.1039	0.4711	-0.1294	-1.2079	0.1786	-1.0004	0.0211	-0.0244	-0.1299	0.5409	-0.0722	0.2	0.5551	-0.1201	0.6079	37.706	-34.807	-33.332
13	2.3946	-0.8636	-1.0754	0.5501	0.219	1.2916	0.2329	0.3446	0.1277	-0.1304	-0.1263	-0.0284	-0.1867	-0.2067	-0.1755	0.355	0.0363	0.0235	0.2984	0.0382	0.345	11.909	-7.566	-18.878
14	1.4091	-0.579	0.76	2.6713	1.4065	2.4519	-0.0661	-0.4729	-0.4166	0.2473	0.4002	0.1953	0.1193	-0.2626	-0.2655	0.3607	0.034	-0.0411	0.8192	0.4965	1.2903	11.535	-15.193	-3.561

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 2:24 )	A	2 - 24
2	X-RAY DIFFRACTION	2	( CHAIN A AND RESID 25:168 )	A	25 - 168
3	X-RAY DIFFRACTION	3	( CHAIN A AND RESID 169:190 )	A	169 - 190
4	X-RAY DIFFRACTION	4	( CHAIN A AND RESID 191:269 )	A	191 - 269
5	X-RAY DIFFRACTION	5	( CHAIN A AND RESID 270:298 )	A	270 - 298
6	X-RAY DIFFRACTION	6	( CHAIN A AND RESID 299:334 )	A	299 - 334
7	X-RAY DIFFRACTION	7	( CHAIN B AND RESID 2:24 )	B	2 - 24
8	X-RAY DIFFRACTION	8	( CHAIN B AND RESID 25:86 )	B	25 - 86
9	X-RAY DIFFRACTION	9	( CHAIN B AND RESID 87:147 )	B	87 - 147
10	X-RAY DIFFRACTION	10	( CHAIN B AND RESID 148:193 )	B	148 - 193
11	X-RAY DIFFRACTION	11	( CHAIN B AND RESID 194:254 )	B	194 - 254
12	X-RAY DIFFRACTION	12	( CHAIN B AND RESID 255:298 )	B	255 - 298
13	X-RAY DIFFRACTION	13	( CHAIN B AND RESID 299:334 )	B	299 - 334
14	X-RAY DIFFRACTION	14	( CHAIN A AND RESID 401:401 ) OR ( CHAIN B AND RESID 401:401 )	A	401
15	X-RAY DIFFRACTION	14	( CHAIN A AND RESID 401:401 ) OR ( CHAIN B AND RESID 401:401 )	B	401

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