PDB-6wbd: Crystal Structure of Lysyl-tRNA synthetase from Stenotrophomonas ...

ID or keywords:

Entry

Database: PDB / ID: 6wbd

Title

Crystal Structure of Lysyl-tRNA synthetase from Stenotrophomonas maltophilia with bound L-lysine

Components

Lysine--tRNA ligase

Keywords

LIGASE / SSGCID / Lysyl-tRNA synthetase / synthetase /

tRNA-ligase /

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 / magnesium ion binding /

ATP binding /

cytoplasm
Similarity search - Function

Biological species

Stenotrophomonas maltophilia (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 2.05 Å

Authors

Seattle Structural Genomics Center for Infectious Disease / Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Citation

Journal: to be published
Title: Crystal Structure of Lysyl-tRNA synthetase from Stenotrophomonas maltophilia with bound L-lysine
Authors: Dranow, D.M. / Lorimer, D.D. / Horanyi, P.S. / Edwards, T.E.

History

Deposition	Mar 26, 2020	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Apr 8, 2020	Provider: repository / Type: Initial release
Revision 1.1	Oct 18, 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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Download

PDBx/mmCIF format	6wbd.cif.gz	491.5 KB	Display	PDBx/mmCIF format
PDB format	pdb6wbd.ent.gz	332.7 KB	Display	PDB format
PDBx/mmJSON format	6wbd.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/wb/6wbd ftp://data.pdbj.org/pub/pdb/validation_reports/wb/6wbd	HTTPS FTP

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Related structure data

Related structure data	1bbuS S: Starting model for refinement
Similar structure data	1lyl-2 1e1o-1 5hgq-1 7ea9-1 1lyl-1 1bbu-1 3e9h-1 5yzx-1 4ex5-d 6aqh-6 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 (6) #227 - Nov 2018 Telomerase similarity (2)

Deposited unit

A: Lysine--tRNA ligase

B: Lysine--tRNA ligase

hetero molecules

119 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)	127.160, 127.160, 158.700
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	152
Space group name H-M	P3₁21
Space group name Hall	P3₁2"
Symmetry operation	#1: x,y,z #2: -y,x-y,z+1/3 #3: -x+y,-x,z+2/3 #4: x-y,-y,-z+2/3 #5: -x,-x+y,-z+1/3 #6: y,x,-z

#1: Protein	Lysine--tRNA ligase / Lysyl-tRNA synthetase / LysRS Mass: 58006.516 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Stenotrophomonas maltophilia (strain K279a) (bacteria) Strain: K279a / Gene: lysS, Smlt2232 / Plasmid: StmaA.00612.a.B1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B2FQ84, lysine-tRNA ligase
#2: Chemical	ChemComp-LYS / LYSINE / Lysine Type: L-peptide linking / Mass: 147.195 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₆H₁₅N₂O₂ / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	... ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol Mass: 62.068 Da / Num. of mol.: 50 / Source method: obtained synthetically / Formula: C₂H₆O₂
#4: Chemical	ChemComp-CL / CHLORIDE ION / Chloride Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 548 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	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: 3.19 Å³/Da / Density % sol: 61.47 %
Crystal grow	Temperature: 287 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: StmaA.00612.a.B1.PW38745 at 10 mg/ml was incubated with 2 mM L-lysine and adenosine, then mixed 1:1 with Morpheus(H6): 10% (w/v) PEG 8000, 20% (v/v) ethylene glycol, 0.1 M MOPS/HEPES-Na pH 7. ...Details: StmaA.00612.a.B1.PW38745 at 10 mg/ml was incubated with 2 mM L-lysine and adenosine, then mixed 1:1 with Morpheus(H6): 10% (w/v) PEG 8000, 20% (v/v) ethylene glycol, 0.1 M MOPS/HEPES-Na pH 7.5, 0.02 M each sodium L-glutamate, DL-alanine, glycine, DL-lysine HCl, DL-serine. Tray 313975h6. Puck xdi4-1.

Crystal

Density Matthews: 3.19 Å³/Da / Density % sol: 61.47 %

Crystal grow

Temperature: 287 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: StmaA.00612.a.B1.PW38745 at 10 mg/ml was incubated with 2 mM L-lysine and adenosine, then mixed 1:1 with Morpheus(H6): 10% (w/v) PEG 8000, 20% (v/v) ethylene glycol, 0.1 M MOPS/HEPES-Na pH 7. ...

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 21-ID-F / Wavelength: 0.97872 Å

Detector

Type: RAYONIX MX-300 / Detector: CCD / Date: Feb 13, 2020 / 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: 2.05→50 Å / Num. obs: 87130 / % possible obs: 93.3 % / Redundancy: 8.035 % / B_iso Wilson estimate: 35.416 Å² / CC_1/2: 0.999 / R_merge(I) obs: 0.08 / R_rim(I) all: 0.085 / Χ²: 1.021 / Net I/σ(I): 17.32

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. unique obs	CC_1/2	R_rim(I) all	% possible all
2.05-2.1	7.897	0.56	3.4	6522	0.878	0.6	95.6
2.1-2.16	7.882	0.447	4.3	6382	0.911	0.478	95.5
2.16-2.22	7.922	0.351	5.52	6168	0.94	0.376	95.3
2.22-2.29	7.936	0.324	5.98	5950	0.953	0.346	94.9
2.29-2.37	7.962	0.264	7.34	5830	0.967	0.283	94.8
2.37-2.45	7.963	0.24	8.14	5603	0.971	0.256	94.5
2.45-2.54	7.993	0.193	9.98	5386	0.982	0.206	94.4
2.54-2.65	8.021	0.164	11.7	5158	0.987	0.176	93.9
2.65-2.76	8.048	0.142	13.36	4932	0.99	0.152	93.7
2.76-2.9	8.066	0.115	16.22	4743	0.993	0.123	93.3
2.9-3.06	8.109	0.093	19.93	4453	0.995	0.1	92.9
3.06-3.24	8.129	0.073	24.42	4240	0.997	0.078	92.6
3.24-3.47	8.161	0.059	29.55	3957	0.998	0.063	92.3
3.47-3.74	8.202	0.05	34.76	3682	0.998	0.053	91.7
3.74-4.1	8.211	0.043	39.75	3384	0.998	0.046	91.1
4.1-4.58	8.238	0.038	43.29	3037	0.999	0.041	90.5
4.58-5.29	8.249	0.037	44.1	2688	0.999	0.04	89.7
5.29-6.48	8.251	0.04	41.4	2269	0.998	0.043	89
6.48-9.17	8.189	0.036	45.66	1768	0.999	0.038	87.9
9.17-50	7.668	0.032	49.58	978	0.999	0.035	83.4

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Phasing

Phasing	Method: molecular replacement

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Processing

Software

Name	Version	Classification
PHENIX	1.17.1-3360	refinement
XDS		data reduction
XSCALE		data scaling
PDB_EXTRACT	3.25	data extraction
MoRDa		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1BBU

1bbu

Resolution: 2.05→41.62 Å / SU ML: 0.1958 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 17.505

	R_factor	Num. reflection	% reflection
R_free	0.1839	4958	5.95 %
R_work	0.1494	-	-
obs	0.1514	83260	89.25 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Displacement parameters

B_iso mean: 37.26 Å²

Refinement step

Cycle: LAST / Resolution: 2.05→41.62 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7503	0	222	548	8273

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0072	7900
X-RAY DIFFRACTION	f_angle_d	0.8054	10612
X-RAY DIFFRACTION	f_chiral_restr	0.0507	1152
X-RAY DIFFRACTION	f_plane_restr	0.005	1394
X-RAY DIFFRACTION	f_dihedral_angle_d	16.7947	2934

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 (%)
2.05-2.07	0.263	168	0.2269	2384	X-RAY DIFFRACTION	82.32
2.07-2.1	0.3028	124	0.2178	2431	X-RAY DIFFRACTION	83.33
2.1-2.12	0.2497	152	0.2056	2473	X-RAY DIFFRACTION	85.37
2.12-2.15	0.2478	164	0.1899	2469	X-RAY DIFFRACTION	85.57
2.15-2.18	0.2236	164	0.183	2510	X-RAY DIFFRACTION	87.73
2.18-2.21	0.2335	177	0.1747	2546	X-RAY DIFFRACTION	87.84
2.21-2.24	0.2035	148	0.1663	2563	X-RAY DIFFRACTION	88.11
2.24-2.27	0.2217	151	0.1685	2558	X-RAY DIFFRACTION	88.15
2.27-2.31	0.2006	158	0.1661	2604	X-RAY DIFFRACTION	88.47
2.31-2.35	0.1837	157	0.1604	2531	X-RAY DIFFRACTION	89.36
2.35-2.39	0.2124	174	0.1557	2642	X-RAY DIFFRACTION	89.97
2.39-2.43	0.1996	150	0.1578	2607	X-RAY DIFFRACTION	89.66
2.43-2.48	0.2028	175	0.1567	2644	X-RAY DIFFRACTION	90.24
2.48-2.53	0.1815	164	0.1522	2581	X-RAY DIFFRACTION	90.21
2.53-2.58	0.1948	169	0.1496	2641	X-RAY DIFFRACTION	90.38
2.58-2.64	0.203	172	0.1455	2649	X-RAY DIFFRACTION	91.06
2.64-2.71	0.1711	166	0.1511	2654	X-RAY DIFFRACTION	90.91
2.71-2.78	0.1978	174	0.1576	2622	X-RAY DIFFRACTION	90.96
2.78-2.86	0.1798	168	0.1497	2666	X-RAY DIFFRACTION	91.15
2.86-2.96	0.1976	151	0.1503	2689	X-RAY DIFFRACTION	91.49
2.96-3.06	0.2121	150	0.151	2696	X-RAY DIFFRACTION	91.9
3.06-3.18	0.1854	188	0.1489	2677	X-RAY DIFFRACTION	91.65
3.18-3.33	0.1599	189	0.1404	2673	X-RAY DIFFRACTION	91.64
3.33-3.5	0.1683	175	0.1339	2678	X-RAY DIFFRACTION	91.53
3.51-3.72	0.1459	151	0.1309	2706	X-RAY DIFFRACTION	91.37
3.72-4.01	0.171	179	0.1242	2656	X-RAY DIFFRACTION	91.04
4.01-4.41	0.1543	182	0.1215	2684	X-RAY DIFFRACTION	90.5
4.42-5.05	0.1476	157	0.1293	2690	X-RAY DIFFRACTION	90.01
5.05-6.36	0.1919	177	0.1629	2679	X-RAY DIFFRACTION	89.03
6.37-41.62	0.1808	184	0.1641	2699	X-RAY DIFFRACTION	86.79

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	1.38568855106	-0.793492673915	-0.966696370901	1.25642234157	0.530109843092	1.13843390392	-0.186627275631	-0.151735257522	-0.20190220704	0.305622618237	0.0837774822994	0.31578357147	0.114874667827	-0.0485869246282	0.095329908902	0.291249452818	0.0596400704199	0.0417769074276	0.185155810304	0.0333879261821	0.260211491902	34.4574659206	18.5769602387	34.6762687056
2	1.00212350372	0.055618708553	0.148406482596	2.11855052706	0.0288686456446	1.20874492629	-0.0227124063552	0.00867747805414	-0.15891463354	0.0113626709778	-0.00866523812952	0.0459080923619	0.103253991401	-0.0963040200119	0.0407953868393	0.187020073869	0.0328310365027	0.000868288664148	0.148180385744	-0.0144823554347	0.208832081097	56.1864822403	-8.40183706666	19.2427407992
3	1.72492419555	-0.32742821703	-1.89921104871	1.15429128811	0.146099447374	2.61260089989	-0.202832151002	0.308634778125	-0.291166196582	-0.18843763477	-0.0451213803307	0.221558089268	0.31305459225	-0.319570648721	0.248469409395	0.292390871767	0.005447006186	-0.0340950116499	0.220616462949	-0.0451276886131	0.264830948719	48.3345381662	3.67711439045	10.6596524657
4	8.02654878657	6.36185987971	2.00262540243	5.17700138512	2.04653994654	2.06747521236	0.157347637069	-0.140998687726	-1.66506151031	-0.20162307079	-0.135758827056	-0.354537547743	0.45689420954	0.057301637822	-0.0662098490922	0.160675002898	0.0102035406159	-0.0105121300533	0.237819899736	-0.0567327096882	0.25489773717	51.7454380856	4.10438490979	13.5195437157
5	3.1767579973	0.555124849458	-0.752222226374	2.11152939571	0.236098342845	1.60477506846	0.0410102394994	0.0636693215552	0.0755852314634	-0.144482256453	-0.101125302895	-0.220922840201	-0.10551114488	0.0643778684625	0.0579960523772	0.253780409201	0.0374190075132	0.0271634096539	0.153377999202	0.0508033216561	0.168232954836	74.0514553698	19.3045839647	2.19087160303
6	1.35191923554	-0.164903126686	-0.87327599208	1.36459294592	0.0819870225447	1.37955525448	-0.0624308143422	0.122390663703	-0.110865081582	-0.065852077271	-0.0163761198422	0.260871404791	0.0336411401899	-0.186946232578	0.0745026872613	0.190486666335	0.0507833974756	-0.0312399283661	0.160408968505	-0.000832919254376	0.251747471034	36.868664075	21.686470987	19.4955902682
7	1.80819642689	-0.0811020088631	-0.558803359069	2.0496743597	-0.245097450197	1.30512414158	-0.0647760263344	0.269400825937	0.087885304251	-0.220927628427	0.0488363780193	0.33476006288	-0.0959192463691	-0.350613003433	0.0357585880677	0.226396124275	0.0653481875073	-0.0572271206472	0.243883178925	-0.00885582734694	0.204345180142	28.3144452611	42.5036048379	17.3427638111
8	2.34613489998	0.0840989309699	-1.75491753582	1.32393043793	-0.306976657771	1.55568382293	-0.0452043187974	0.505576577797	-0.0479911657304	-0.179118017013	0.0414173047191	0.420700492	0.103922294875	-0.478869695468	0.00660857188526	0.258167716651	0.0270056475259	-0.082703111468	0.308928365485	-0.0232711607248	0.342710585467	28.7869604153	25.7567425965	17.2941928063
9	6.39025308854	-4.92911406216	-2.47640015816	6.40497429347	2.89932373511	2.24929789136	0.190010445824	0.179990303214	0.907468879818	-0.560538845677	0.688009735274	0.193444505018	-1.58817783869	-2.17319291686	-0.883782749717	0.280894441171	0.058716598741	-0.0668059333427	0.22897966807	-0.00406025501874	0.186237627354	30.381680197	28.5740214189	20.502633177

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 11 through 284 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 285 through 430 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 431 through 499 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 601 through 601 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 11 through 175 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 176 through 284 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 285 through 430 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 431 through 501 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 1003 through 1003 )

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