PDB-4j76: Crystal Structure of a parasite tRNA synthetase, ligand-free

ID or keywords:

Entry

Database: PDB / ID: 4j76

Title

Crystal Structure of a parasite tRNA synthetase, ligand-free

Components

Tryptophanyl-tRNA synthetase

Keywords

LIGASE /

aminoacyl-tRNA synthetase / aaRS /

TrpRS /

parasite / protein-substrate complex /

Rossmann fold /

translation /

nucleotide binding

Function / homology

Function and homology information

tryptophan-tRNA ligase /

tryptophan-tRNA ligase activity / tryptophanyl-tRNA aminoacylation /

ATP binding /

cytoplasm
Similarity search - Function

Biological species

Plasmodium falciparum (malaria parasite P. falciparum)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 2.34 Å

Authors

Koh, C.Y. / Kim, J.E. / Verlinde, C.L.M.J. / Hol, W.G.J.

Citation

Journal: Mol.Biochem.Parasitol. / Year: 2013
Title: Crystal structures of Plasmodium falciparum cytosolic tryptophanyl-tRNA synthetase and its potential as a target for structure-guided drug design.
Authors: Koh, C.Y. / Kim, J.E. / Napoli, A.J. / Verlinde, C.L. / Fan, E. / Buckner, F.S. / Van Voorhis, W.C. / Hol, W.G.

History

Deposition	Feb 12, 2013	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	May 22, 2013	Provider: repository / Type: Initial release
Revision 1.1	May 29, 2013	Group: Database references
Revision 1.2	Jun 12, 2013	Group: Database references
Revision 1.3	Sep 20, 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 / 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 / _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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PDBx/mmCIF format	4j76.cif.gz	317.3 KB	Display	PDBx/mmCIF format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/j7/4j76 ftp://data.pdbj.org/pub/pdb/validation_reports/j7/4j76	HTTPS FTP

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Related structure data

Related structure data	4j75C 3hv0S S: Starting model for refinement C: citing same article (ref.)
Similar structure data	4j75-d 4jfa-2 2quh-d 2quj-d 1ulh-d 4jfa-1 3hzr-3 3tze-d 2quk-1 1o5t-1 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	#16 - Apr 2001 Aminoacyl-tRNA Synthetases similarity (2)

Deposited unit

A: Tryptophanyl-tRNA synthetase

B: Tryptophanyl-tRNA synthetase

hetero molecules

94.8 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)	117.301, 190.669, 51.732
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	18
Space group name H-M	P2₁2₁2

Components on special symmetry positions

ID	Model	Components
1	1	B-908- HOH

#1: Protein	Tryptophanyl-tRNA synthetase / Tryptophan--tRNA ligase Mass: 47216.734 Da / Num. of mol.: 2 / Fragment: UNP residues 229-632 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum) Strain: 3D7 / Gene: PF13_0205 / Plasmid: AVA0421 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8IDW3, tryptophan-tRNA ligase
#2: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₃H₈O₃
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 324 / 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: 3.06 Å³/Da / Density % sol: 59.84 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop Details: 0.2 M sodium citrate, 20% PEG3350, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

ALS

/ Beamline: 5.0.2 / Wavelength: 0.977

Detector

Type: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 25, 2010

Radiation

Monochromator: liquid N2 cooled double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.977 Å / Relative weight: 1

Reflection

Resolution: 2.34→50 Å / Num. obs: 49735 / % possible obs: 100 % / Redundancy: 7.3 % / R_merge(I) obs: 0.088 / Χ²: 1.004 / Net I/σ(I): 11.5

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique all	Χ²	Diffraction-ID	% possible all
2.34-2.38	6.5	0.363	2412	0.954	1	100
2.38-2.42	7.3	0.346	2427	0.974	1	100
2.42-2.47	7.4	0.3	2488	0.969	1	100
2.47-2.52	7.4	0.277	2410	0.967	1	100
2.52-2.58	7.4	0.251	2484	0.983	1	100
2.58-2.64	7.4	0.222	2424	0.979	1	100
2.64-2.7	7.4	0.197	2471	1.021	1	100
2.7-2.77	7.4	0.17	2444	1.02	1	100
2.77-2.86	7.4	0.141	2491	1.064	1	100
2.86-2.95	7.4	0.13	2426	1.081	1	100
2.95-3.05	7.4	0.109	2502	1	1	100
3.05-3.18	7.4	0.096	2442	1.037	1	100
3.18-3.32	7.4	0.079	2478	0.977	1	100
3.32-3.5	7.3	0.07	2478	1.007	1	100
3.5-3.71	7.3	0.064	2506	0.974	1	100
3.71-4	7.3	0.066	2517	0.969	1	100
4-4.4	7.2	0.081	2497	1.068	1	100
4.4-5.04	7.2	0.095	2532	0.987	1	100
5.04-6.35	6.9	0.072	2576	1.054	1	100
6.35-50	6.7	0.029	2730	0.998	1	100

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Phasing

Phasing

Method:

molecular replacement

Phasing MR

R_factor: 57.91 / Model details: Phaser MODE: MR_AUTO

	Highest resolution	Lowest resolution
Rotation	2.5 Å	49.95 Å
Translation	2.5 Å	49.95 Å

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Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
PHASER	2.1.4	phasing
REFMAC	refmac_5.7.0032	refinement
PDB_EXTRACT	3.11	data extraction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3HV0

3hv0

Resolution: 2.34→30 Å / Cor.coef. F_o:F_c: 0.953 / Cor.coef. F_o:F_c free: 0.932 / WR_factor R_free: 0.209 / WR_factor R_work: 0.179 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 9.232 / SU ML: 0.114 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.232 / ESU R Free: 0.184 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2094	2506	5.1 %	RANDOM
R_work	0.1793	-	-	-
obs	0.1808	49504	99.42 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK

Displacement parameters

B_iso max: 163.78 Å² / B_iso mean: 45.8473 Å² / B_iso min: 16.5 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.12 Å²	-0 Å²	0 Å²
2-	-	-0.03 Å²	0 Å²
3-	-	-	0.15 Å²

Refinement step

Cycle: LAST / Resolution: 2.34→30 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5959	0	24	324	6307

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.007	0.019	6160
X-RAY DIFFRACTION	r_bond_other_d	0.003	0.02	5896
X-RAY DIFFRACTION	r_angle_refined_deg	1.077	1.961	8305
X-RAY DIFFRACTION	r_angle_other_deg	0.843	3	13614
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.51	5	732
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	36.162	24.901	304
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.586	15	1125
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	16.013	15	18
X-RAY DIFFRACTION	r_chiral_restr	0.063	0.2	893
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.021	6909
X-RAY DIFFRACTION	r_gen_planes_other	0.003	0.02	1475
X-RAY DIFFRACTION	r_mcbond_it	0.585	1.703	2913
X-RAY DIFFRACTION	r_mcbond_other	0.584	1.702	2912
X-RAY DIFFRACTION	r_mcangle_it	1.005	2.55	3635

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
2.34-2.404	0.276	170	0.217	3285	3570	96.779
2.404-2.469	0.246	186	0.2	3339	3542	99.52
2.469-2.54	0.201	173	0.201	3185	3372	99.585
2.54-2.618	0.215	171	0.195	3182	3366	99.614
2.618-2.703	0.25	155	0.189	3062	3231	99.567
2.703-2.797	0.23	169	0.183	2929	3109	99.646
2.797-2.902	0.189	151	0.176	2886	3045	99.737
2.902-3.019	0.185	177	0.182	2708	2895	99.655
3.019-3.152	0.196	136	0.181	2647	2793	99.642
3.152-3.304	0.224	135	0.175	2546	2691	99.628
3.304-3.48	0.2	127	0.185	2441	2575	99.728
3.48-3.688	0.233	117	0.178	2312	2439	99.59
3.688-3.939	0.194	95	0.168	2180	2278	99.868
3.939-4.248	0.163	102	0.158	2052	2157	99.861
4.248-4.644	0.174	91	0.146	1889	1985	99.748
4.644-5.177	0.199	103	0.155	1717	1825	99.726
5.177-5.948	0.218	71	0.2	1528	1602	99.813
5.948-7.215	0.29	78	0.232	1328	1410	99.716
7.215-9.92	0.197	67	0.159	1055	1125	99.733
9.92-30	0.218	31	0.202	699	730	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	5.5351	1.1376	-0.571	3.7884	0.4848	1.6801	-0.0781	0.2027	0.531	-0.1923	0.0526	0.243	-0.2472	-0.1069	0.0255	0.0612	0.0051	-0.0215	0.0857	0.022	0.0587	10.669	10.1	7.236
2	0.9905	-0.1316	-0.6607	0.765	0.41	2.4522	-0.0046	0.0413	0.0649	-0.0179	-0.0093	-0.004	-0.1223	-0.0498	0.014	0.0112	-0.0071	-0.0114	0.0598	0.014	0.0239	28.717	3.161	-2.798
3	2.7663	-0.9501	-0.3081	9.6629	4.7887	2.4762	-0.0679	0.5369	0.1511	-1.2107	0.0695	-0.0813	-0.5574	0.0011	-0.0015	0.1991	-0.0805	0.0078	0.2327	0.0414	0.0862	13.709	4.738	-2.028
4	17.3636	-13.1956	-2.2911	10.1871	1.6464	0.4081	0.4013	0.6384	-1.4081	-0.787	-0.375	1.1211	0.2604	-0.2594	-0.0263	1.4736	-0.4263	-0.2737	1.5442	-0.062	0.936	18.381	28.627	-6.61
5	7.9342	-3.1863	0.6636	6.3951	-0.2943	2.1154	-0.1504	0.5306	1.3558	-0.417	0.0297	-0.3231	-0.4697	-0.0736	0.1207	0.3864	-0.0489	-0.044	0.1388	0.033	0.4949	14.471	35.494	3.818
6	4.0255	-3.2634	0.7752	7.0167	-1.0461	1.0454	-0.2746	-0.4428	0.645	0.4647	0.2928	0.0689	-0.2727	-0.0381	-0.0182	0.2031	-0.0315	-0.0106	0.2161	-0.0813	0.1951	20.614	21.314	14.149
7	11.9579	-2.6109	7.277	6.34	-4.6274	14.8931	0.3163	1.2037	-0.7448	-1.1708	0.0675	-0.3279	0.7666	0.0956	-0.3838	0.4339	0.0366	0.1798	0.3598	-0.1214	0.3474	60.348	-19.563	-26.913
8	2.8468	-0.9254	0.0759	1.7743	-0.4045	0.8339	0.0247	0.1356	-0.5177	-0.0697	-0.0159	-0.0746	0.3561	0.0144	-0.0088	0.1604	0.0024	-0.0214	0.088	-0.0249	0.1391	44.472	-16.09	-12.331
9	2.7395	-2.4918	-0.6133	8.6504	-1.0346	1.729	0.0814	0.3285	-0.2882	-0.7392	-0.2122	0.3596	0.3297	-0.1667	0.1308	0.1064	-0.0034	0.019	0.2016	-0.0052	0.1216	49.125	-11.231	-20.602
10	7.6664	-0.8213	-0.0888	5.449	-0.2197	13.1052	-0.2084	1.2109	-0.8286	-1.5899	0.4245	0.2556	0.6506	-0.6572	-0.2161	0.8092	-0.1793	-0.1331	0.36	-0.2048	0.9498	40.775	-42.765	-24.733
11	0.0041	-0.0051	-0.0204	0.0279	0.0653	0.1837	-0.0379	-0.0456	-0.0271	0.1277	0.16	-0.1229	0.4471	0.3572	-0.1221	2.0355	0.0461	0.1083	1.4205	-0.6953	1.4643	53.776	-39.505	-36.12
12	3.0686	0.4031	0.5067	5.9303	2.4236	4.8481	0.0224	0.3943	-1.1665	-0.4258	0.3351	-0.6846	0.6425	0.4869	-0.3576	0.371	0.0724	-0.0613	0.256	-0.0929	0.6489	52.691	-35.018	-14.852

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	244 - 334
2	X-RAY DIFFRACTION	2	A	335 - 443
3	X-RAY DIFFRACTION	3	A	444 - 487
4	X-RAY DIFFRACTION	4	A	488 - 512
5	X-RAY DIFFRACTION	5	A	513 - 566
6	X-RAY DIFFRACTION	6	A	567 - 632
7	X-RAY DIFFRACTION	7	B	244 - 275
8	X-RAY DIFFRACTION	8	B	276 - 443
9	X-RAY DIFFRACTION	9	B	444 - 485
10	X-RAY DIFFRACTION	10	B	486 - 537
11	X-RAY DIFFRACTION	11	B	551 - 552
12	X-RAY DIFFRACTION	12	B	553 - 632

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