PDB-3p0h: Leishmania major Tyrosyl-tRNA synthetase in complex with fisetin,...

ID or keywords:

Entry

Database: PDB / ID: 3p0h

Title

Leishmania major Tyrosyl-tRNA synthetase in complex with fisetin, cubic crystal form

Components

Tyrosyl-tRNA synthetase

Keywords

LIGASE / aminoacyl-tRNA synthetase / tRNA ligase / aaRS / TyrRS / pseudodimer / translation / ATP-binding / nucleotide-binding / Structural Genomics / Medical Structural Genomics of Pathogenic Protozoa / MSGPP

Function / homology

Function and homology information

tyrosyl-tRNA aminoacylation / tyrosine-tRNA ligase / tyrosine-tRNA ligase activity / ciliary plasm / ATP binding / cytoplasm
Similarity search - Function

Biological species

Leishmania major (eukaryote)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT,

SAD /

molecular replacement /

SAD / Resolution: 3 Å

Authors

Larson, E.T. / Merritt, E.A. / Medical Structural Genomics of Pathogenic Protozoa (MSGPP)

Citation

Journal: J.Mol.Biol. / Year: 2011
Title: The Double-Length Tyrosyl-tRNA Synthetase from the Eukaryote Leishmania major Forms an Intrinsically Asymmetric Pseudo-Dimer.
Authors: Larson, E.T. / Kim, J.E. / Castaneda, L.J. / Napuli, A.J. / Zhang, Z. / Fan, E. / Zucker, F.H. / Verlinde, C.L. / Buckner, F.S. / Van Voorhis, W.C. / Hol, W.G. / Merritt, E.A.

History

Deposition	Sep 28, 2010	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Mar 23, 2011	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Version format compliance
Revision 1.2	Nov 8, 2017	Group: Refinement description / Category: software / Item: _software.name
Revision 1.3	Sep 6, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif / struct_site Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4	Dec 6, 2023	Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.5	Nov 27, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	3p0h.cif.gz	500.8 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	3p0h_validation.pdf.gz	951.5 KB	Display	wwPDB validaton report
Full document	3p0h_full_validation.pdf.gz	967.7 KB	Display
Data in XML	3p0h_validation.xml.gz	43.8 KB	Display
Data in CIF	3p0h_validation.cif.gz	58.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/p0/3p0h ftp://data.pdbj.org/pub/pdb/validation_reports/p0/3p0h	HTTPS FTP

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Related structure data

Related structure data	3p0iC 3p0jC 2cyaS 2cycS 2j5bS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	3p0j-4 3p0j-3 3p0j-1 3p0i-1 1o5t-1 3k8l-1 3a04-1 3a05-1 2quk-1 4u0z-3 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	#16 - Apr 2001 Aminoacyl-tRNA Synthetases similarity (1)

Deposited unit

A: Tyrosyl-tRNA synthetase

B: Tyrosyl-tRNA synthetase

hetero molecules

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

1

A: Tyrosyl-tRNA synthetase

hetero molecules

defined by author&software
77.3 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Tyrosyl-tRNA synthetase

hetero molecules

defined by author&software
77.3 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	240.240, 240.240, 240.240
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	197
Space group name H-M	I23

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	B
2	1	A

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Refine code	Auth asym-ID	Auth seq-ID
1	1	1	4	B	0 - 355
2	1	1	4	A	0 - 355
1	2	1	4	B	370 - 488
2	2	1	4	A	370 - 488
1	3	1	4	B	493 - 555
2	3	1	4	A	493 - 555
1	4	1	4	B	567 - 600
2	4	1	4	A	567 - 600
1	5	1	4	B	625 - 681
2	5	1	4	A	625 - 681

#1: Protein	Tyrosyl-tRNA synthetase Mass: 77057.195 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Leishmania major (eukaryote) / Gene: LmjF14.1370 / Plasmid: BG1861 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q4QFJ7, tyrosine-tRNA ligase
#2: Chemical	ChemComp-FSE / 3,7,3',4'-TETRAHYDROXYFLAVONE / Fisetin / 2-(3,4-DIHYDROXYPHENYL)-3,7-DIHYDROXY-4H-CHROMEN-4-ONE Mass: 286.236 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₅H₁₀O₆
Has protein modification	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 3.75 Å³/Da / Density % sol: 67.19 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, sitting drop Details: equal volumes SeMet protein solution (24 mg/ml LmTyrRS in MSGPP buffer containing 5 mM DTT and 5 mM fisetin) and well solution (25% PEG 3350, 0.1 M tri-sodium citrate pH 5.5, and 4% w/v ...Details: equal volumes SeMet protein solution (24 mg/ml LmTyrRS in MSGPP buffer containing 5 mM DTT and 5 mM fisetin) and well solution (25% PEG 3350, 0.1 M tri-sodium citrate pH 5.5, and 4% w/v acetone); cryoprotected by addition of 30% PEG 3350, 10% MSGPP buffer, 10% ethylene glycol, and 0.1 M tri-sodium citrate pH 5.5 directly to drop prior to mounting and freezing crystals in liquid nitrogen, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal

Density Matthews: 3.75 Å³/Da / Density % sol: 67.19 %

Crystal grow

Temperature: 277 K / Method: vapor diffusion, sitting drop
Details: equal volumes SeMet protein solution (24 mg/ml LmTyrRS in MSGPP buffer containing 5 mM DTT and 5 mM fisetin) and well solution (25% PEG 3350, 0.1 M tri-sodium citrate pH 5.5, and 4% w/v ...

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

SSRL

/ Beamline: BL9-2 / Wavelength: 0.97931 Å

Detector

Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Mar 19, 2010

Radiation

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

Radiation wavelength

Wavelength: 0.97931 Å / Relative weight: 1

Reflection

Resolution: 3→47.11 Å / Num. obs: 46076 / % possible obs: 99.95 % / Redundancy: 13.81 % / B_iso Wilson estimate: 75 Å² / R_merge(I) obs: 0.155 / Net I/σ(I): 14.0489

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. measured all	Num. unique all	Diffraction-ID	% possible all
3-3.16	10.48	0.016	70153	6696	1	99.84
3.16-3.35	13.58	0.016	85962	6329	1	100
3.35-3.59	13.84	0.016	82428	5954	1	100
3.59-3.87	14.08	0.016	77710	5520	1	100
3.87-4.24	14.43	0.016	73521	5096	1	100
4.24-4.74	14.95	0.016	69464	4646	1	100
4.74-5.48	15.13	0.016	62228	4113	1	100
5.48-6.71	15.08	0.016	52459	3479	1	100
6.71-9.49	14.9	0.016	40519	2719	1	100
9.49-47.11	14.32	0.016	21828	1524	1	99.09

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Phasing

Phasing

Method
molecular replacement
SAD

Phasing dm

FOM : 0.76 / FOM acentric: 0.76 / FOM centric: 0.69 / Reflection: 46076 / Reflection acentric: 43572 / Reflection centric: 2504

Phasing dm shell

Resolution (Å)	FOM	FOM acentric	FOM centric	Reflection	Reflection acentric	Reflection centric
8.6-47.115	0.96	0.97	0.89	2062	1765	297
5.4-8.6	0.86	0.87	0.74	6204	5724	480
4.3-5.4	0.85	0.86	0.7	7703	7255	448
3.8-4.3	0.77	0.78	0.66	7779	7399	380
3.2-3.8	0.67	0.67	0.6	13759	13181	578
3-3.2	0.67	0.67	0.62	8569	8248	321

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Processing

Software

Name	Version	Classification
MOSFLM		data reduction
SCALA	CCP4_3.3.9	data scaling
RESOLVE	2.13	phasing
REFMAC	refmac_5.5.0110	refinement
PDB_EXTRACT	3.1	data extraction
Blu-Ice		data collection
BALBES		phasing
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT,

SAD
Starting model: Initial partial MR solution with PDB entry 2j5b, then determined experimental phases and heavy atom positions by SAD. Also used PDB entries 2cya and 2cyc to aid in model completion.

2j5b

2cya

2cyc

Resolution: 3→47.11 Å / Cor.coef. F_o:F_c: 0.921 / Cor.coef. F_o:F_c free: 0.895 / WR_factor R_free: 0.25 / WR_factor R_work: 0.215 / Occupancy max: 1 / Occupancy min: 0.4 / SU B: 39.529 / SU ML: 0.324 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.394 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2727	2329	5.1 %	RANDOM
R_work	0.2336	-	-	-
obs	0.2355	46076	99.97 %	-

Solvent computation

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

Displacement parameters

B_iso max: 266.36 Å² / B_iso mean: 80.8342 Å² / B_iso min: 29.54 Å²

Refinement step

Cycle: LAST / Resolution: 3→47.11 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	9723	0	42	0	9765

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.006	0.022	9945
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	6642
X-RAY DIFFRACTION	r_angle_refined_deg	0.898	1.969	13465
X-RAY DIFFRACTION	r_angle_other_deg	0.763	3	16253
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	4.873	5	1256
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	33.048	24.514	432
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.068	15	1746
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	15.338	15	63
X-RAY DIFFRACTION	r_chiral_restr	0.052	0.2	1544
X-RAY DIFFRACTION	r_gen_planes_refined	0.003	0.02	11047
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1904
X-RAY DIFFRACTION	r_mcbond_it	1.702	4	6283
X-RAY DIFFRACTION	r_mcbond_other	0.236	4	2553
X-RAY DIFFRACTION	r_mcangle_it	2.934	6	10060
X-RAY DIFFRACTION	r_scbond_it	2.087	6	3662
X-RAY DIFFRACTION	r_scangle_it	3.615	10	3401

Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: B / Ens-ID: 1 / Number: 7569 / Refine-ID: X-RAY DIFFRACTION

Type	Rms dev position (Å)	Weight position
MEDIUM POSITIONAL	0.41	0.5
MEDIUM THERMAL	0.84	2

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 (%)
3-3.078	0.363	183	0.326	3189	3386	99.587
3.078-3.162	0.352	185	0.307	3131	3316	100
3.162-3.253	0.334	152	0.295	2995	3147	100
3.253-3.353	0.346	147	0.272	2968	3115	100
3.353-3.462	0.285	167	0.261	2845	3012	100
3.462-3.583	0.312	137	0.249	2782	2919	100
3.583-3.717	0.277	159	0.242	2669	2828	100
3.717-3.868	0.275	153	0.235	2565	2718	100
3.868-4.039	0.29	110	0.226	2464	2574	100
4.039-4.234	0.264	124	0.218	2380	2504	100
4.234-4.461	0.255	122	0.196	2256	2378	100
4.461-4.729	0.202	108	0.182	2151	2259	100
4.729-5.052	0.22	118	0.184	1993	2111	100
5.052-5.452	0.251	96	0.184	1895	1991	100
5.452-5.964	0.214	85	0.195	1729	1814	100
5.964-6.655	0.258	70	0.226	1597	1667	100
6.655-7.659	0.285	61	0.229	1421	1482	100
7.659-9.319	0.236	65	0.216	1189	1254	100
9.319-12.928	0.264	52	0.251	948	1000	100
12.928-47.115	0.366	35	0.386	580	615	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	1.7377	1.17	0.2997	0.4822	0.0977	0.3591	0.0392	-0.0729	-0.2345	0.0256	-0.1322	-0.1637	0.0055	-0.0653	0.0929	0.1222	0.0345	0.116	0.0898	0.1143	0.4752	22.539	67.515	64.514
2	2.4857	0.9135	-0.1519	1.0484	0.2092	1.1797	0.3448	0.0094	0.0874	0.2464	-0.2339	-0.0339	0.0341	-0.0874	-0.1109	0.0324	-0.0558	0.055	0.0575	0.0323	0.1241	-24.166	45.547	68.912
3	0.8557	-0.0772	-0.3082	1.2792	0.381	0.117	-0.0794	0.1649	0.045	0.0399	0.0307	0.0097	-0.0001	-0.0719	0.0487	0.1278	0.064	0.0821	0.1898	0.0538	0.3713	4.15	91.828	42.473
4	1.8514	-1.2233	-1.353	0.2815	0.401	1.1342	-0.0383	0.927	-0.4125	0.1936	-0.3989	0.0926	0.1859	-0.6154	0.4373	0.0946	-0.0645	0.1989	0.6676	-0.3139	0.3598	17.724	61.924	9.647

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	-1 - 358
2	X-RAY DIFFRACTION	2	A	365 - 681
3	X-RAY DIFFRACTION	3	B	-2 - 355
4	X-RAY DIFFRACTION	4	B	366 - 681

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