PDB-5eln: Crystal Structure of Lysyl-tRNA Synthetase from Cryptosporidium p...

ID or keywords:

Entry

Database: PDB / ID: 5eln

Title

Crystal Structure of Lysyl-tRNA Synthetase from Cryptosporidium parvum complexed with L-lysine

Components

Lysine--tRNA ligase

Keywords

LIGASE / SSGCID / Lysine--tRNA ligase /

Cryptosporidium parvum /

ATP binding /

aminoacylation /

Structural Genomics / Seattle Structural Genomics Center for Infectious Disease

Function / homology

Function and homology information

lysine-tRNA ligase /

lysine-tRNA ligase activity / lysyl-tRNA aminoacylation /

nucleic acid binding /

ATP binding /

membrane /

cytoplasm
Similarity search - Function

Biological species

Cryptosporidium parvum (eukaryote)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 1.9 Å

Authors

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Citation

Journal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2019
Title: Lysyl-tRNA synthetase as a drug target in malaria and cryptosporidiosis.
Authors: Baragana, B. / Forte, B. / Choi, R. / Nakazawa Hewitt, S. / Bueren-Calabuig, J.A. / Pisco, J.P. / Peet, C. / Dranow, D.M. / Robinson, D.A. / Jansen, C. / Norcross, N.R. / Vinayak, S. / ...

History

Deposition	Nov 4, 2015	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Nov 16, 2016	Provider: repository / Type: Initial release
Revision 1.1	Apr 3, 2019	Group: Data collection / Database references / Derived calculations Category: citation / citation_author / pdbx_struct_oper_list Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2	Sep 27, 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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PDBx/mmCIF format	5eln.cif.gz	838.4 KB	Display	PDBx/mmCIF format
PDB format	pdb5eln.ent.gz	696.9 KB	Display	PDB format
PDBx/mmJSON format	5eln.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/el/5eln ftp://data.pdbj.org/pub/pdb/validation_reports/el/5eln	HTTPS FTP

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Related structure data

Related structure data	5eloC 6agtC 6hcuC 6hcvC 6hcwC 3bjuS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	6c86-d 5zh4-d 6ka6-2 6kab-1 6ild-d 3bju-3 6kcn-2 6hcw-d 4pg3-1 1bbu-1 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
Other databases	TargetTrack: SSGCID-CrpaA.00612.a

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#16 - Apr 2001 Aminoacyl-tRNA Synthetases similarity (7) #227 - Nov 2018 Telomerase similarity (2)

Deposited unit

A: Lysine--tRNA ligase

B: Lysine--tRNA ligase

C: Lysine--tRNA ligase

D: Lysine--tRNA ligase

hetero molecules

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

1

A: Lysine--tRNA ligase

B: Lysine--tRNA ligase

hetero molecules

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

2

C: Lysine--tRNA ligase

D: Lysine--tRNA ligase

hetero molecules

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

Unit cell

Length a, b, c (Å)	72.920, 119.450, 143.630
Angle α, β, γ (deg.)	90.00, 90.31, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Lysine--tRNA ligase / Lysyl-tRNA synthetase Mass: 61459.094 Da / Num. of mol.: 4 / Fragment: CrpaA.00612.a.A3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Cryptosporidium parvum (strain Iowa II) (eukaryote) Strain: Iowa II / Gene: cgd4_2370 / Plasmid: CrpaA.00612.a.A3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q5CR27, lysine-tRNA ligase
#2: Chemical	ChemComp-LYS / LYSINE / Lysine Type: L-peptide linking / Mass: 147.195 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₆H₁₅N₂O₂
#3: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C₂H₆O₂
#4: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₈O₃
#5: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 1942 / 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: 2.54 Å³/Da / Density % sol: 51.66 %
Crystal grow	Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: CrpaA.00612.a.A3.PW37710 at 35 mg/ml, protein was incubated with 3 mM MgCl2, L-lysine, and AMPPNP, then mixed 1:1 with Index(g5): 25% (w/v) PEG-3350, 0.2 M lithium sulfate, 0.1 M Tris base/ ...Details: CrpaA.00612.a.A3.PW37710 at 35 mg/ml, protein was incubated with 3 mM MgCl2, L-lysine, and AMPPNP, then mixed 1:1 with Index(g5): 25% (w/v) PEG-3350, 0.2 M lithium sulfate, 0.1 M Tris base/ HCl, pH = 8.5, cryoprotected with 20% ethylene glycol

Crystal

Density Matthews: 2.54 Å³/Da / Density % sol: 51.66 %

Crystal grow

Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: CrpaA.00612.a.A3.PW37710 at 35 mg/ml, protein was incubated with 3 mM MgCl2, L-lysine, and AMPPNP, then mixed 1:1 with Index(g5): 25% (w/v) PEG-3350, 0.2 M lithium sulfate, 0.1 M Tris base/ ...

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
Detector	Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 25, 2015 / Details: Beryllium Lenses
Radiation	Monochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97872 Å / Relative weight: 1
Reflection	Resolution: 1.9→50 Å / Num. obs: 192804 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 3.8 % / B_iso Wilson estimate: 20.37 Å² / R_merge(I) obs: 0.081 / Net I/σ(I): 11.89
Reflection shell	Resolution: 1.9→1.95 Å / Redundancy: 3.8 % / R_merge(I) obs: 0.474 / Mean I/σ(I) obs: 2.82 / % possible all: 99.9

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Phasing

Phasing	Method: molecular replacement

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Processing

Software

Name	Version	Classification
PHENIX		refinement
XSCALE		data scaling
PHASER	2.5.7	phasing
PDB_EXTRACT	3.15	data extraction
XDS		data reduction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3BJU

3bju

Resolution: 1.9→19.98 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 18.54 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.192	9616	4.99 %
R_work	0.154	-	-
obs	0.156	192621	99.7 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso mean: 25.96 Å²

Refinement step

Cycle: LAST / Resolution: 1.9→19.98 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	15969	0	82	1942	17993

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	16710
X-RAY DIFFRACTION	f_angle_d	0.889	22613
X-RAY DIFFRACTION	f_dihedral_angle_d	13.238	10215
X-RAY DIFFRACTION	f_chiral_restr	0.055	2443
X-RAY DIFFRACTION	f_plane_restr	0.006	2929

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 (%)
1.9-1.9215	0.2811	327	0.2362	6124	X-RAY DIFFRACTION	100
1.9215-1.9441	0.2652	325	0.2174	6069	X-RAY DIFFRACTION	100
1.9441-1.9678	0.268	293	0.2151	6115	X-RAY DIFFRACTION	100
1.9678-1.9927	0.2419	296	0.2024	6071	X-RAY DIFFRACTION	100
1.9927-2.0189	0.2526	268	0.1907	6136	X-RAY DIFFRACTION	100
2.0189-2.0465	0.2239	294	0.1878	6115	X-RAY DIFFRACTION	100
2.0465-2.0757	0.2344	356	0.1837	6052	X-RAY DIFFRACTION	100
2.0757-2.1067	0.2241	369	0.1803	5988	X-RAY DIFFRACTION	100
2.1067-2.1396	0.2288	317	0.1767	6139	X-RAY DIFFRACTION	100
2.1396-2.1746	0.2094	295	0.1667	6102	X-RAY DIFFRACTION	100
2.1746-2.2121	0.2217	340	0.1666	6096	X-RAY DIFFRACTION	100
2.2121-2.2522	0.2066	341	0.1621	6028	X-RAY DIFFRACTION	100
2.2522-2.2955	0.2073	321	0.1642	6074	X-RAY DIFFRACTION	100
2.2955-2.3423	0.2142	304	0.1615	6090	X-RAY DIFFRACTION	100
2.3423-2.3931	0.1985	313	0.1572	6066	X-RAY DIFFRACTION	100
2.3931-2.4487	0.1972	304	0.1576	6128	X-RAY DIFFRACTION	100
2.4487-2.5098	0.2078	345	0.1561	6065	X-RAY DIFFRACTION	100
2.5098-2.5775	0.2146	347	0.1538	6015	X-RAY DIFFRACTION	100
2.5775-2.6532	0.1991	295	0.1577	6117	X-RAY DIFFRACTION	100
2.6532-2.7387	0.2133	338	0.159	6079	X-RAY DIFFRACTION	100
2.7387-2.8363	0.1838	315	0.1546	6098	X-RAY DIFFRACTION	100
2.8363-2.9495	0.2036	311	0.1529	6102	X-RAY DIFFRACTION	100
2.9495-3.0833	0.1863	296	0.1594	6143	X-RAY DIFFRACTION	100
3.0833-3.2452	0.2012	385	0.1572	6050	X-RAY DIFFRACTION	100
3.2452-3.4475	0.1805	359	0.1504	6086	X-RAY DIFFRACTION	100
3.4475-3.7121	0.1846	286	0.1417	6162	X-RAY DIFFRACTION	100
3.7121-4.0828	0.147	318	0.1296	6154	X-RAY DIFFRACTION	100
4.0828-4.6671	0.1502	314	0.1167	6138	X-RAY DIFFRACTION	100
4.6671-5.8554	0.1506	335	0.1274	6146	X-RAY DIFFRACTION	100
5.8554-19.9835	0.1518	309	0.1483	6257	X-RAY DIFFRACTION	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	1.3249	0.1958	0.2967	1.1083	0.3787	0.6093	0.1379	-0.1458	0.0314	0.2679	-0.1613	0.1791	0.1372	-0.1126	0.0049	0.1903	-0.0483	0.0392	0.1536	-0.0033	0.144	50.141	93.667	21.819
2	1.4754	0.3993	-0.0647	1.0003	-0.1404	1.3997	0.039	-0.0289	0.0562	0.0953	0.0195	-0.0077	-0.0914	0.1038	-0.0534	0.1324	0.0121	-0.0113	0.1119	0.0172	0.1488	82.295	120.726	19.078
3	0.5508	0.2658	0.2532	1.0759	-0.0584	0.7508	-0.0541	-0.0442	0.0604	0.0635	0.0616	0.1284	-0.2231	-0.0288	-0.0012	0.1624	0.0183	0.0054	0.2101	0.0186	0.1193	78.92	136.109	11.986
4	1.084	0.306	-0.4785	1.064	-0.4185	0.8496	0.0406	0.4213	-0.2017	-0.0346	-0.1885	-0.4007	0.0713	0.5165	0.0559	0.107	0.0261	0.0384	0.5852	0.0191	0.3343	110.893	124.619	3.66
5	1.5063	0.308	0.2113	1.1284	0.3361	0.6969	0.0673	-0.0815	0.0704	0.2042	-0.0441	-0.0531	0.0699	0.0503	-0.0274	0.1552	0.0016	-0.0156	0.106	0.0172	0.1097	78.972	108.909	26.378
6	0.5793	0.0589	0.0574	0.3851	-0.2495	0.3846	0.0393	-0.059	-0.073	0.1365	-0.0332	-0.1063	0.055	0.0424	-0.0046	0.2551	-0.012	-0.0383	0.1625	-0.0095	0.1992	82.637	94.743	35.376
7	1.3874	0.0775	-0.0079	1.2221	0.6515	2.9129	0.0576	0.029	0.1206	-0.057	-0.0418	0.1707	0.0039	-0.1912	-0.0124	0.1149	-0.017	-0.0066	0.0834	0.0322	0.1907	48.284	66.437	50.368
8	1.0888	-0.6271	0.3598	0.7711	-0.324	0.3226	0.0388	0.0911	-0.1166	-0.0753	-0.0155	0.0962	0.065	0.003	-0.0196	0.1335	-0.0143	0.0124	0.0895	-0.0081	0.1224	75.243	38.573	51.314
9	0.7464	-0.0788	0.1621	0.6459	-0.1674	0.6793	0.013	-0.0011	-0.2499	-0.0701	0.0397	0.0939	0.183	-0.0813	-0.004	0.1609	-0.0298	0.0027	0.0985	0.0049	0.1868	78.756	20.79	60.729
10	1.2987	-0.536	0.1798	0.6792	-0.2218	0.5568	-0.0052	-0.0051	0.0863	-0.0139	-0.0351	-0.1955	0.0208	0.1631	0.0395	0.1192	-0.03	0.01	0.1198	0.001	0.1613	97.133	38.663	59.17
11	0.3236	-0.0499	-0.026	0.5871	-0.2766	0.5115	0.0078	0.177	0.0497	-0.1224	-0.0345	-0.0824	0.0024	0.0675	0.0289	0.1536	-0.0014	0.0127	0.1722	0.0254	0.1519	81.12	60.779	34.888

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 45:209 )	A	45 - 209
2	X-RAY DIFFRACTION	2	( CHAIN A AND RESID 210:318 )	A	210 - 318
3	X-RAY DIFFRACTION	3	( CHAIN A AND ( RESID 319:545 OR RESID 601:601 ) )	A	319 - 545
4	X-RAY DIFFRACTION	3	( CHAIN A AND ( RESID 319:545 OR RESID 601:601 ) )	A	601
5	X-RAY DIFFRACTION	4	( CHAIN B AND RESID 45:209 )	B	45 - 209
6	X-RAY DIFFRACTION	5	( CHAIN B AND RESID 210:318 )	B	210 - 318
7	X-RAY DIFFRACTION	6	( CHAIN B AND ( RESID 319:545 OR RESID 601:601 ) )	B	319 - 545
8	X-RAY DIFFRACTION	6	( CHAIN B AND ( RESID 319:545 OR RESID 601:601 ) )	B	601
9	X-RAY DIFFRACTION	7	( CHAIN C AND RESID 45:173 )	C	45 - 173
10	X-RAY DIFFRACTION	8	( CHAIN C AND RESID 174:318 )	C	174 - 318
11	X-RAY DIFFRACTION	9	( CHAIN C AND ( RESID 319:545 OR RESID 601:601 ) )	C	319 - 545
12	X-RAY DIFFRACTION	9	( CHAIN C AND ( RESID 319:545 OR RESID 601:601 ) )	C	601
13	X-RAY DIFFRACTION	10	( CHAIN D AND RESID 45:318 )	D	45 - 318
14	X-RAY DIFFRACTION	11	( CHAIN D AND ( RESID 319:545 OR RESID 601:601 ) )	D	319 - 545
15	X-RAY DIFFRACTION	11	( CHAIN D AND ( RESID 319:545 OR RESID 601:601 ) )	D	601

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