PDB-5y0s: Crystal structure of apo Thermotoga maritima TmcAL(Form II)

ID or keywords:

Entry

Database: PDB / ID: 5y0s

Title

Crystal structure of apo Thermotoga maritima TmcAL(Form II)

Components

Thermotoga maritima TmcAL

Keywords

LIGASE / acetate ligase

Function / homology

Function and homology information

Ligases; Forming carbon-nitrogen bonds; Other carbon-nitrogen ligases / ligase activity, forming carbon-nitrogen bonds / tRNA modification / tRNA binding / ATP binding / cytoplasm
Similarity search - Function

Biological species

Thermotoga maritima (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.103 Å

Authors

Yamashita, S. / Tomita, K.

Citation

Journal: Nat. Chem. Biol. / Year: 2018
Title: Acetate-dependent tRNA acetylation required for decoding fidelity in protein synthesis.
Authors: Taniguchi, T. / Miyauchi, K. / Sakaguchi, Y. / Yamashita, S. / Soma, A. / Tomita, K. / Suzuki, T.

History

Deposition	Jul 18, 2017	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Jul 18, 2018	Provider: repository / Type: Initial release
Revision 1.1	Dec 26, 2018	Group: Data collection / Database references / Structure summary Category: citation / citation_author / struct_keywords Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _struct_keywords.pdbx_keywords / _struct_keywords.text
Revision 1.2	Nov 22, 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	5y0s.cif.gz	701.2 KB	Display	PDBx/mmCIF format
PDB format	pdb5y0s.ent.gz	586.1 KB	Display	PDB format
PDBx/mmJSON format	5y0s.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	5y0s_validation.pdf.gz	483 KB	Display	wwPDB validaton report
Full document	5y0s_full_validation.pdf.gz	497.6 KB	Display
Data in XML	5y0s_validation.xml.gz	64.3 KB	Display
Data in CIF	5y0s_validation.cif.gz	90.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/y0/5y0s ftp://data.pdbj.org/pub/pdb/validation_reports/y0/5y0s	HTTPS FTP

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Related structure data

Related structure data	5y0nC 5y0oC 5y0pC 5y0qC 5y0rSC 5y0tC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	5y0t-1 5y0r-1 5y0t-2 3t20-2 5y0o-d 6s65-d 5hrm-2 3iuc-d 5ioj-d 6s6g-d 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

Deposited unit

A: Thermotoga maritima TmcAL

B: Thermotoga maritima TmcAL

C: Thermotoga maritima TmcAL

D: Thermotoga maritima TmcAL

hetero molecules

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

1

A: Thermotoga maritima TmcAL

B: Thermotoga maritima TmcAL

hetero molecules

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

2

C: Thermotoga maritima TmcAL

D: Thermotoga maritima TmcAL

hetero molecules

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

Unit cell

Length a, b, c (Å)	80.990, 97.954, 144.279
Angle α, β, γ (deg.)	90.000, 99.180, 90.000
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Thermotoga maritima TmcAL Mass: 49466.934 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: The CDS of Tm TmcAL (and stop codon) is cloned into pET22b with NdeI and XhoI sites. Any tags are not included in the expressed sequence. Source: (gene. exp.) Thermotoga maritima (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: Q9X1K1*PLUS
#2: Chemical	... ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 22 / Source method: obtained synthetically / Formula: C₂H₆O₂
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 622 / Source method: isolated from a natural source / Formula: H₂O
Sequence details	Our sequence is based on WP_024103782.1.

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.86 Å³/Da / Density % sol: 56.92 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: Tris, PEG8000, NaCl

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Data collection

Diffraction

Mean temperature: 95 K

Diffraction source

Source:

SYNCHROTRON / Site:

Photon Factory

/ Beamline: BL-17A / Wavelength: 0.98 Å

Detector

Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 25, 2014

Radiation

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

Radiation wavelength

Wavelength: 0.98 Å / Relative weight: 1

Reflection

Resolution: 2.1→50 Å / Num. obs: 128895 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 6.8 % / B_iso Wilson estimate: 31.59 Å² / R_merge(I) obs: 0.13 / R_rim(I) all: 0.141 / Χ²: 0.989 / Net I/σ(I): 12.09

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Highest resolution (Å)	R_merge(I) obs	Mean I/σ(I) obs	Num. unique obs	R_rim(I) all	% possible all
2.1-2.16		1.225	1.61	9229	1.328	96.9
2.16-2.22		1.004	2.01	9265	1.088	100
2.22-2.28		0.824	2.54	9037	0.891	99.9
2.28-2.35		0.669	3.09	8760	0.724	100
2.35-2.43		0.535	3.79	8494	0.581	99.9
2.43-2.51		0.444	4.61	8229	0.48	100
2.51-2.61		0.381	5.19	7959	0.414	99.9
2.61-2.72		0.314	6.34	7634	0.34	99.9
2.72-2.84		0.239	8.25	7308	0.259	100
2.84-2.97		0.198	9.54	7013	0.215	99.9
2.97-3.14		0.154	12.36	6682	0.166	100
3.14-3.33		0.117	15.43	6307	0.127	100
3.33-3.56		0.086	20.35	5949	0.093	99.9
3.56-3.84		0.066	25.51	5538	0.072	100
3.84-4.21		0.053	30.44	5100	0.058	99.9
4.21-4.7		0.046	35.11	4633	0.05	100
4.7-5.43		0.048	34.45	4091	0.052	99.8
5.43-6.65		0.052	30.96	3464	0.057	100
6.65-9.41		0.036	39.49	2686	0.039	99.7
	9.41	0.027	48.29	1517	0.03	98.8

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Processing

Software

Name	Version	Classification
XSCALE		data scaling
PHENIX	1.8.4_1496	refinement
PDB_EXTRACT	3.15	data extraction
XDS		data reduction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5Y0R

5y0r

Resolution: 2.103→49.889 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 21.74

	R_factor	Num. reflection	% reflection
R_free	0.2074	6444	5 %
R_work	0.1688	-	-
obs	0.1707	128886	99.72 %

Solvent computation

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

Displacement parameters

B_iso max: 180.51 Å² / B_iso mean: 44.19 Å² / B_iso min: 13.33 Å²

Refinement step

Cycle: final / Resolution: 2.103→49.889 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	13848	0	88	622	14558
B_iso mean	-	-	52.75	39.67	-
Num. residues	-	-	-	-	1692

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	14214
X-RAY DIFFRACTION	f_angle_d	1.055	19040
X-RAY DIFFRACTION	f_chiral_restr	0.045	2032
X-RAY DIFFRACTION	f_plane_restr	0.005	2452
X-RAY DIFFRACTION	f_dihedral_angle_d	14.101	5370

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
2.1032-2.1271	0.3136	202	0.2819	3842	4044	93
2.1271-2.1521	0.2816	213	0.2604	4057	4270	100
2.1521-2.1783	0.3042	214	0.2479	4065	4279	100
2.1783-2.2059	0.2791	213	0.2383	4046	4259	100
2.2059-2.2349	0.2786	215	0.2328	4083	4298	100
2.2349-2.2656	0.2845	215	0.2302	4079	4294	100
2.2656-2.2979	0.2766	213	0.213	4046	4259	100
2.2979-2.3322	0.2588	216	0.2134	4110	4326	100
2.3322-2.3687	0.2551	214	0.1947	4062	4276	100
2.3687-2.4075	0.2331	214	0.1923	4068	4282	100
2.4075-2.449	0.2514	216	0.1867	4096	4312	100
2.449-2.4935	0.244	215	0.1872	4089	4304	100
2.4935-2.5415	0.2347	214	0.1887	4063	4277	100
2.5415-2.5934	0.2299	215	0.1855	4081	4296	100
2.5934-2.6498	0.226	215	0.1805	4089	4304	100
2.6498-2.7114	0.2579	214	0.1798	4080	4294	100
2.7114-2.7792	0.2094	213	0.1719	4043	4256	100
2.7792-2.8543	0.2271	215	0.1689	4072	4287	100
2.8543-2.9383	0.2181	215	0.1794	4100	4315	100
2.9383-3.0331	0.2268	216	0.1806	4087	4303	100
3.0331-3.1415	0.2382	215	0.1781	4099	4314	100
3.1415-3.2673	0.2199	217	0.1819	4114	4331	100
3.2673-3.416	0.2096	215	0.1769	4080	4295	100
3.416-3.596	0.1933	214	0.1663	4077	4291	100
3.596-3.8212	0.1872	216	0.1568	4101	4317	100
3.8212-4.1162	0.1655	217	0.1382	4132	4349	100
4.1162-4.5301	0.1514	217	0.1242	4115	4332	100
4.5301-5.1851	0.1684	217	0.1249	4112	4329	100
5.1851-6.5303	0.1905	218	0.1544	4148	4366	100
6.5303-49.9026	0.1492	221	0.1405	4206	4427	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	1.3631	-0.1185	0.4026	1.235	0.0586	2.8839	-0.0342	-0.0018	0.1074	0.046	0.0116	-0.1156	-0.1523	0.2579	0.0316	0.1227	-0.0174	-0.0062	0.1917	-0.004	0.2251	55.7783	77.4176	126.3596
2	2.5323	-1.0505	0.4398	7.4948	-0.7609	2.409	0.0143	0.2091	0.6355	-0.153	-0.1007	-0.233	-0.4955	0.2315	0.0323	0.3037	-0.0634	-0.0132	0.2677	0.0169	0.3453	50.9162	99.1033	132.9193
3	5.8197	-0.4249	-3.9717	8.7232	4.1575	4.4517	-0.1514	-0.207	0.7225	-0.6311	0.2928	-0.3904	-1.0746	0.6297	-0.1518	0.7455	-0.1567	-0.0694	0.7007	0.0277	0.5026	69.9081	87.777	118.1946
4	0.4384	0.1446	0.1065	1.0764	-0.1757	1.8283	-0.0179	0.06	0.077	-0.0787	-0.02	0.0368	-0.189	0.1008	0.0252	0.1739	-0.018	-0.0209	0.193	0.0124	0.2236	48.863	78.3666	112.9757
5	3.0702	-0.6615	0.2864	0.4007	0.1964	2.2263	0.0971	0.2054	-0.0418	-0.329	-0.1	0.0137	0.0177	-0.0604	-0.0046	0.4304	0.0391	-0.0368	0.2096	0.0358	0.227	31.9225	83.993	69.5924
6	5.0536	1.0813	-3.3291	8.2982	-1.1657	2.8161	-0.519	0.1104	-0.7044	0.3195	0.0382	0.3958	0.711	-0.0529	0.4629	0.6335	0.0392	-0.0884	0.3736	-0.0822	0.3886	14.7894	68.9665	73.3765
7	3.4971	-0.048	-5.3645	4.9335	1.0576	8.4612	-0.051	0.1907	0.0676	0.5466	0.1972	0.0843	-0.382	-0.927	-0.1476	0.9307	0.0725	0.0166	0.8889	0.013	0.8269	40.9952	67.2485	66.7234
8	0.7538	-0.2446	0.5368	1.4154	-0.3209	1.5587	0.0712	-0.0185	0.0262	-0.1512	-0.0412	-0.0319	-0.1057	0.0048	-0.0248	0.3026	-0.0102	-0.029	0.2366	0.0407	0.2294	37.0675	83.6655	83.6677
9	3.0648	0.0674	-1.1958	0.7441	0.2523	2.533	-0.0827	-0.1905	-0.055	0.0774	0.0196	0.0914	0.0309	0.0309	0.0639	0.1487	0.0208	0.0059	0.1846	0.0316	0.2646	21.8313	33.8913	145.4922
10	1.8939	-2.4351	0.4502	5.8848	-1.1884	3.0941	0.1365	0.0967	0.2381	-0.2713	-0.1105	-0.3359	-0.4034	0.0814	-0.0093	0.2075	-0.0211	0.0661	0.2563	-0.004	0.3989	5.613	47.6693	136.7319
11	5.7561	-6.9713	5.131	9.0377	-6.5542	4.7862	1.002	0.0158	0.0334	-0.396	0.5486	0.9615	0.4727	-0.6918	-1.4969	1.0187	0.1225	-0.092	1.0795	0.0612	1.0228	27.6649	51.6092	149.8199
12	1.2999	0.2805	-0.798	1.3136	-0.2636	1.1077	-0.0833	-0.0247	-0.0461	-0.0424	0.059	0.1187	0.0961	-0.0105	0.0231	0.1718	0.0106	-0.0122	0.2138	0.0087	0.2603	31.0488	34.4079	133.671
13	1.5371	0.4215	-0.3337	1.0821	0.3999	2.2292	-0.115	0.0843	-0.1528	-0.5012	0.015	-0.2883	0.4524	0.4448	0.0789	0.445	0.0993	0.0895	0.3112	0.0089	0.2526	62.7018	42.421	99.613
14	4.9587	0.8275	2.1537	2.3121	0.0758	2.312	0.3181	-0.1199	-1.7432	-0.5796	-0.0924	-0.6395	1.2601	0.147	-0.2319	1.2685	0.1014	0.2703	0.5084	0.0071	1.0157	62.7219	20.7316	93.0261
15	2.7928	-3.2497	-2.5545	7.1414	0.6984	7.5234	-0.089	-0.0169	0.1208	-1.0147	0.8156	-1.1694	1.5179	0.4359	-0.6878	1.3226	0.2559	0.2256	1.174	0.2297	1.1911	74.775	34.254	112.6002
16	0.6605	0.2655	-0.4348	1.5306	-0.7475	1.2973	-0.0773	0.0287	-0.0538	-0.3913	0.0113	-0.0083	0.3529	0.077	0.0463	0.3032	0.0363	0.0071	0.2088	-0.0195	0.1993	51.5493	40.6806	109.6462

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 1:107)	A	1 - 107
2	X-RAY DIFFRACTION	2	(chain A and resid 108:193)	A	108 - 193
3	X-RAY DIFFRACTION	3	(chain A and resid 194:206)	A	194 - 206
4	X-RAY DIFFRACTION	4	(chain A and resid 207:423)	A	207 - 423
5	X-RAY DIFFRACTION	5	(chain B and resid 1:107)	B	1 - 107
6	X-RAY DIFFRACTION	6	(chain B and resid 108:193)	B	108 - 193
7	X-RAY DIFFRACTION	7	(chain B and resid 194:206)	B	194 - 206
8	X-RAY DIFFRACTION	8	(chain B and resid 207:423)	B	207 - 423
9	X-RAY DIFFRACTION	9	(chain C and resid 1:107)	C	1 - 107
10	X-RAY DIFFRACTION	10	(chain C and resid 108:193)	C	108 - 193
11	X-RAY DIFFRACTION	11	(chain C and resid 194:206)	C	194 - 206
12	X-RAY DIFFRACTION	12	(chain C and resid 207:423)	C	207 - 423
13	X-RAY DIFFRACTION	13	(chain D and resid 1:107)	D	1 - 107
14	X-RAY DIFFRACTION	14	(chain D and resid 108:193)	D	108 - 193
15	X-RAY DIFFRACTION	15	(chain D and resid 194:206)	D	194 - 206
16	X-RAY DIFFRACTION	16	(chain D and resid 207:423)	D	207 - 423

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