PDB-3n9i: Crystal structure of tryptophanyl-tRNA synthetase from Yersinia p...

ID or keywords:

Entry

Database: PDB / ID: 3n9i

Title

Crystal structure of tryptophanyl-tRNA synthetase from Yersinia pestis CO92

Components

Tryptophanyl-tRNA synthetase

Keywords

LIGASE / tryptophanyl-tRNA synthetase / Tryptophan-tRNA ligase / CSGID / Structural Genomics / NIAID / Center for Structural Genomics of Infectious Diseases

Function / homology

Function and homology information

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

Biological species

Yersinia pestis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.95 Å

Authors

Nocek, B. / Maltseva, N. / Papazisi, L. / Anderson, W. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)

Citation

Journal: TO BE PUBLISHED
Title: Crystal structure of tryptophanyl-tRNA synthetase from Yersinia pestis CO92
Authors: Nocek, B. / Maltseva, N. / Papazisi, L. / Anderson, W. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)

History

Deposition	May 30, 2010	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jul 21, 2010	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Version format compliance
Revision 1.2	Oct 1, 2014	Group: Structure summary
Revision 1.3	Sep 6, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3n9i.cif.gz	288.2 KB	Display	PDBx/mmCIF format
PDB format	pdb3n9i.ent.gz	236 KB	Display	PDB format
PDBx/mmJSON format	3n9i.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	3n9i_validation.pdf.gz	448.2 KB	Display	wwPDB validaton report
Full document	3n9i_full_validation.pdf.gz	453.8 KB	Display
Data in XML	3n9i_validation.xml.gz	28.9 KB	Display
Data in CIF	3n9i_validation.cif.gz	43 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/n9/3n9i ftp://data.pdbj.org/pub/pdb/validation_reports/n9/3n9i	HTTPS FTP

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Related structure data

Related structure data	3fi0S S: Starting model for refinement
Similar structure data	6dfu-d 2g36-1 3tzl-d 1maw-1 1mb2-1 3fi0-3 1mb2-2 3m5w-d 3fhj-1 2ih3-d 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	TargetDB: idp90591

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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)

Deposited unit

A: Tryptophanyl-tRNA synthetase

B: Tryptophanyl-tRNA synthetase

hetero molecules

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

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	61.099, 78.150, 152.176
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Tryptophanyl-tRNA synthetase / Tryptophan--tRNA ligase / TrpRS Mass: 38714.211 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Yersinia pestis (bacteria) / Strain: CO92 / Gene: trpS, YPO0157, y3940, YP_0159 / Production host: Cricetulus griseus (Chinese hamster) / Strain (production host): BL21 magic / References: UniProt: Q8ZJF2, tryptophan-tRNA ligase
#2: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₈O₃
#3: Chemical	ChemComp-CA / CALCIUM ION Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 445 / 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: 2.35 Å³/Da / Density % sol: 47.57 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 0.2 M Ca(oAc)2 0.1 M Tris 20% PEG3000, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 9, 2010 / Details: mirrors
Radiation	Monochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9794 Å / Relative weight: 1
Reflection	Resolution: 1.95→40 Å / Num. all: 55745 / Num. obs: 53290 / % possible obs: 99.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.4 % / R_merge(I) obs: 0.077 / Net I/σ(I): 9.3
Reflection shell	Resolution: 1.95→1.98 Å / Redundancy: 5.3 % / R_merge(I) obs: 0.65 / Mean I/σ(I) obs: 2.8 / Num. unique all: 2581 / % possible all: 98.4

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Processing

Software

Name	Version	Classification
SBC-Collect		data collection
PHASER		phasing
REFMAC	5.5.0109	refinement
HKL-3000		data reduction
HKL-3000		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3FI0

3fi0

Resolution: 1.95→40 Å / Cor.coef. F_o:F_c: 0.96 / Cor.coef. F_o:F_c free: 0.941 / SU B: 6.855 / SU ML: 0.089 / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / ESU R Free: 0.138 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.20615	2693	5.1 %	RANDOM
R_work	0.16707	-	-	-
all	0.18	53040	-	-
obs	0.16905	50347	98.66 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 22.724 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.28 Å²	0 Å²	0 Å²
2-	-	0.75 Å²	0 Å²
3-	-	-	-0.47 Å²

Refinement step

Cycle: LAST / Resolution: 1.95→40 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5209	0	7	445	5661

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.016	0.022	5338
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	3655
X-RAY DIFFRACTION	r_angle_refined_deg	1.42	1.975	7226
X-RAY DIFFRACTION	r_angle_other_deg	0.907	3	8933
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.276	5	670
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	37.311	24.472	246
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.712	15	951
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	18.84	15	36
X-RAY DIFFRACTION	r_chiral_restr	0.097	0.2	806
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.021	5947
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1041
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	0.893	1.5	3326
X-RAY DIFFRACTION	r_mcbond_other	0.235	1.5	1339
X-RAY DIFFRACTION	r_mcangle_it	1.661	2	5353
X-RAY DIFFRACTION	r_scbond_it	2.691	3	2012
X-RAY DIFFRACTION	r_scangle_it	4.459	4.5	1870
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 1.952→2.003 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.279	192	-
R_work	0.222	3487	-
obs	-	-	94.33 %

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	1.2717	0.3609	-0.852	0.3593	-0.1822	0.5846	-0.0531	-0.1039	0.0036	-0.1144	0.055	-0.0085	0.017	0.0887	-0.0019	0.1063	0.0108	-0.0468	0.115	0.0153	0.1464	31.0166	73.517	14.595
2	11.2157	-1.0064	2.995	0.8191	-0.8187	1.2158	0.1036	0.063	-0.3285	-0.2225	-0.0246	-0.0021	0.1889	0.0269	-0.079	0.0787	0.011	0.0031	0.1538	-0.051	0.1083	36.5176	73.2138	5.591
3	0.908	0.4476	0.3094	0.5882	0.2894	0.7573	0.0493	-0.0002	-0.0743	0.0058	0.0068	-0.0772	-0.0599	0.021	-0.0561	0.0908	0.0091	0.0026	0.0902	-0.0045	0.1158	30.0641	77.8856	22.7704
4	1.1515	0.5781	-0.5628	0.454	-0.218	0.5588	0.0311	0.0653	0.0276	-0.022	0.0237	-0.0032	-0.021	-0.008	-0.0548	0.0961	0.017	0.0012	0.0853	0.0069	0.099	25.2964	79.1415	17.794
5	4.2788	0.2151	0.6301	0.8201	-0.0382	1.1881	0.047	0.0875	-0.1182	0.048	-0.0011	-0.2016	0.0793	0.1219	-0.0459	0.1066	0.0154	-0.0215	0.076	0.0089	0.1399	25.5045	59.1178	31.7064
6	2.5401	-0.4487	3.4427	0.3747	-0.8775	4.9148	0.0277	0.3171	-0.1173	0.0585	-0.0792	-0.2148	-0.0192	0.4315	0.0515	0.088	0.0021	-0.0388	0.1341	0.0091	0.1961	29.9851	66.9005	33.319
7	0.8688	0.1785	-0.6865	1.1874	-0.5019	1.3897	-0.0312	0.0574	-0.1011	-0.0048	0.0487	-0.0966	0.101	0.087	-0.0175	0.0883	0.0057	-0.0185	0.0934	-0.0317	0.1256	19.6032	61.6021	18.008
8	0.5163	-0.2266	-1.8901	0.115	0.8517	6.9562	-0.1843	0.5183	-0.1866	0.008	-0.3136	0.0251	0.2467	-1.8453	0.4979	0.0791	-0.0802	0.1242	0.6564	-0.2515	0.2766	36.5197	63.5629	5.7488
9	1.5211	0.3745	2.0975	1.5379	-0.8945	4.372	0.0833	-0.1324	-0.0768	0.04	0.0426	0.1172	0.143	-0.2377	-0.126	0.0832	0.0084	0.0358	0.1163	0.0078	0.1477	51.5899	68.0967	17.7118
10	1.4182	-1.2002	-0.2107	1.2262	0.3629	1.6912	0.0129	0.0424	0.0132	0.0803	-0.0497	0.0528	0.1343	0.2778	0.0368	0.078	0.0227	-0.0046	0.1571	0.0258	0.0737	58.2761	71.6156	9.0956
11	1.9969	-1.1937	0.2218	1.2684	0.2186	2.8547	0.0657	0.0904	-0.0506	-0.1478	0.0211	0.1559	0.3401	0.2753	-0.0868	0.139	0.0466	-0.0198	0.1374	-0.0153	0.0676	56.1741	67.0316	-0.5326
12	3.3684	-3.4668	-1.6151	3.6999	1.3258	1.6676	0.0795	0.0131	0.0229	-0.073	-0.0697	-0.0033	-0.0622	0.173	-0.0098	0.0633	0.0064	-0.0009	0.1354	0.0171	0.0905	54.189	78.6273	4.9778
13	8.8204	-3.3833	-2.7304	2.3714	0.3721	4.1501	0.2937	0.1222	0.2872	-0.1201	-0.1336	-0.0834	-0.1587	0.1347	-0.1601	0.0863	-0.0036	0.0144	0.0668	0.0124	0.1309	37.7541	91.2201	12.4175
14	3.4151	3.6008	0.2823	4.1958	0.1611	0.1932	0.0089	0.0918	0.0942	-0.0298	0.0692	0.1275	-0.0579	-0.0549	-0.0781	0.0917	0.0219	0.0111	0.0862	0.0257	0.1158	19.6195	84.5822	14.9688
15	3.3518	-0.7302	-1.2774	0.3412	-0.2621	2.1751	-0.0333	0.0618	0.077	0.0229	0.0177	-0.0357	-0.1134	-0.1577	0.0156	0.0881	0.0001	-0.0087	0.0962	0.0228	0.0966	4.4301	71.1533	23.5492
16	1.7011	0.7073	1.8968	0.3832	1.046	2.8752	0.3595	-0.3756	-0.1151	0.14	-0.0856	-0.0944	0.3289	-0.2622	-0.2739	0.1961	-0.0197	0.0363	0.1574	0.0227	0.0638	2.4783	76.6865	43.899
17	1.7789	3.5825	-0.5703	11.7237	-4.2656	2.3403	0.2307	-0.3405	-0.1055	0.7154	-0.3775	-0.3913	-0.2751	-0.0947	0.1468	0.2264	-0.0846	0.1054	0.1279	-0.0322	0.1047	-6.2062	77.1726	51.1951
18	0.3582	0.0134	-0.1634	2.3093	1.189	1	0.0808	-0.1691	-0.0304	0.1569	-0.0259	0.1507	-0.0196	-0.0701	-0.0548	0.1134	0.0046	0.0345	0.1716	0.0536	0.1077	3.9731	77.3396	41.2394
19	1.2827	0.2354	-0.2212	0.0564	-0.0275	0.5555	0.0553	-0.0035	0.0365	0.0477	-0.0092	0.0001	-0.0189	-0.0548	-0.0461	0.1232	0.0054	0.0095	0.0819	0.0247	0.0984	1.2575	75.2414	35.1076
20	1.0388	1.4276	-0.529	6.0809	-1.8069	2.0315	0.1749	-0.166	-0.0993	0.4452	-0.1497	-0.139	-0.0195	-0.0638	-0.0252	0.1193	-0.037	-0.07	0.1373	0.0398	0.091	23.2858	65.7804	43.8843
21	4.296	-1.0118	4.8028	6.0559	-4.9647	9.9215	0.106	-0.058	-0.0165	0.1933	0.1123	0.2316	0.1505	-0.2245	-0.2183	0.0897	0.0103	-0.0061	0.0651	0.0201	0.1547	18.3221	51.5899	41.1516
22	0.7097	-0.511	-0.1632	2.1524	0.8221	0.3286	0.0096	-0.1186	-0.0242	0.1593	-0.0116	0.0727	0.0359	0.0004	0.002	0.1329	-0.0161	0.013	0.1067	0.0101	0.0851	13.6371	74.6458	42.0396
23	3.1368	0.3812	-0.9481	2.0674	-0.5454	1.3507	0.0484	-0.3055	-0.0205	0.2589	-0.0076	-0.0069	0.06	-0.038	-0.0408	0.1603	-0.0413	-0.0227	0.1393	-0.0139	0.0169	19.3753	78.2226	48.1635
24	53.0983	24.0192	-29.8648	10.8763	-13.4954	16.8262	1.5297	0.0312	2.1298	0.7132	-0.1674	0.952	-1.0276	-0.0934	-1.3623	0.6569	0.0086	0.4296	0.6229	-0.0205	0.3051	1.1257	78.4764	59.3293
25	2.5607	-0.3563	1.659	3.1149	1.1489	4.0447	-0.0206	0.1897	0.082	-0.1044	-0.0092	-0.2754	0.1766	0.5989	0.0298	0.0957	0.0266	0.0229	0.1652	0.0155	0.0789	-7.1962	60.8709	55.9087
26	0.6724	0.1961	-0.2173	1.382	0.1863	2.1089	0.0305	-0.0239	-0.0167	-0.0291	-0.0089	0.1028	0.238	0.0293	-0.0216	0.0988	-0.0175	0.0126	0.0967	-0.0066	0.0874	-18.3346	61.8012	58.5197
27	0.4414	-0.314	-0.6164	1.7777	0.4358	1.7576	0.0094	-0.098	0.1478	0.0624	0.0282	-0.1213	0.019	0.0933	-0.0376	0.1042	-0.011	0.0159	0.124	-0.0338	0.083	-15.7013	71.2103	67.9234
28	0.9692	0.8618	-2.0029	1.0666	-2.5971	7.1055	0.0571	0.1131	0.1059	0.0805	0.0548	0.0878	-0.1622	-0.3731	-0.1119	0.105	0.003	0.0246	0.1104	-0.0053	0.0946	-19.8523	71.1838	50.8954
29	10.4055	4.15	2.1518	1.7356	0.7574	1.2603	-0.0752	0.1798	0.2009	-0.0479	0.0958	0.0553	-0.1387	-0.0675	-0.0206	0.1114	0.0265	0.0255	0.0752	0.0372	0.1092	-1.0163	83.8706	31.1354
30	1.6176	-0.1826	-0.4665	1.283	-1.3896	1.7845	0.1199	-0.0255	0.0835	0.0678	-0.0163	0.0528	-0.1315	0.0405	-0.1036	0.1281	-0.0124	0.0164	0.0726	-0.0132	0.1048	23.3678	86.4528	30.7942

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	15 - 29
2	X-RAY DIFFRACTION	2	A	30 - 45
3	X-RAY DIFFRACTION	3	A	46 - 70
4	X-RAY DIFFRACTION	4	A	71 - 107
5	X-RAY DIFFRACTION	5	A	108 - 126
6	X-RAY DIFFRACTION	6	A	127 - 145
7	X-RAY DIFFRACTION	7	A	146 - 188
8	X-RAY DIFFRACTION	8	A	189 - 197
9	X-RAY DIFFRACTION	9	A	198 - 218
10	X-RAY DIFFRACTION	10	A	219 - 249
11	X-RAY DIFFRACTION	11	A	250 - 281
12	X-RAY DIFFRACTION	12	A	282 - 301
13	X-RAY DIFFRACTION	13	A	302 - 311
14	X-RAY DIFFRACTION	14	A	312 - 331
15	X-RAY DIFFRACTION	15	A	332 - 346
16	X-RAY DIFFRACTION	16	B	15 - 27
17	X-RAY DIFFRACTION	17	B	28 - 44
18	X-RAY DIFFRACTION	18	B	45 - 61
19	X-RAY DIFFRACTION	19	B	62 - 106
20	X-RAY DIFFRACTION	20	B	107 - 123
21	X-RAY DIFFRACTION	21	B	124 - 133
22	X-RAY DIFFRACTION	22	B	134 - 157
23	X-RAY DIFFRACTION	23	B	158 - 189
24	X-RAY DIFFRACTION	24	B	190 - 196
25	X-RAY DIFFRACTION	25	B	197 - 219
26	X-RAY DIFFRACTION	26	B	220 - 245
27	X-RAY DIFFRACTION	27	B	246 - 279
28	X-RAY DIFFRACTION	28	B	280 - 308
29	X-RAY DIFFRACTION	29	B	309 - 331
30	X-RAY DIFFRACTION	30	B	332 - 346

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