PDB-5y0p: Crystal structure of Bacillus subtilis TmcAL bound with alpha-thio ATP

ID or keywords:

Entry

Database: PDB / ID: 5y0p

Title

Crystal structure of Bacillus subtilis TmcAL bound with alpha-thio ATP

Components

UPF0348 protein B4417_3650

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

Bacillus subtilis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.3 Å

Authors

Yamashita, S. / Tomita, K.

Funding support

Japan, 1items

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	5y0p.cif.gz	339.8 KB	Display	PDBx/mmCIF format
PDB format	pdb5y0p.ent.gz	276.2 KB	Display	PDB format
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Validation report

Summary document	5y0p_validation.pdf.gz	1.3 MB	Display	wwPDB validaton report
Full document	5y0p_full_validation.pdf.gz	1.3 MB	Display
Data in XML	5y0p_validation.xml.gz	31.9 KB	Display
Data in CIF	5y0p_validation.cif.gz	43.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/y0/5y0p ftp://data.pdbj.org/pub/pdb/validation_reports/y0/5y0p	HTTPS FTP

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Related structure data

Related structure data	5y0nSC 5y0oC 5y0qC 5y0rC 5y0sC 5y0tC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	5y0q-d 5y0n-d 5y0o-d 4bld-1 6vwa-1 2dtt-d 3fiw-d 2nsp-d 2g7k-d 1qjv-d 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	#251 - Nov 2020 Adenylyl Cyclase similarity (1)

Deposited unit

A: UPF0348 protein B4417_3650

B: UPF0348 protein B4417_3650

hetero molecules

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

1

Idetical with deposited unit
defined by author

Unit cell

Length a, b, c (Å)	67.995, 67.999, 211.168
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	UPF0348 protein B4417_3650 Mass: 49086.867 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: The gene was cloned into pET15b with NdeI and XhoI site, and expressed as a N-terminally His-tagged protein. Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: B4417_3650 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A164SIT4, UniProt: O34513*PLUS
#2: Chemical	ChemComp-TAT / ADENOSINE-5'-RP-ALPHA-THIO-TRIPHOSPHATE Mass: 523.247 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₀H₁₆N₅O₁₂P₃S
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 67 / 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: 2.49 Å³/Da / Density % sol: 50.53 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: Tris-HCl, PEG400, KCl, MgCl2

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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 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 twin

Operator: -k,-h,-l / Fraction: 0.5

Reflection

Resolution: 2.3→50 Å / Num. obs: 44459 / % possible obs: 99.79 % / Observed criterion σ(I): -3 / Redundancy: 12.83 % / R_merge(I) obs: 0.076 / R_pim(I) all: 0.022 / Χ²: 1.097 / Net I/σ(I): 20.46

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. unique obs	R_pim(I) all	% possible all	R_rim(I) all
2.3-2.34	12.42	1.884	1.3	2137	0.548	95.87
2.34-2.38	13.02	1.569	1.6	2135	0.432	100
2.38-2.43	13.21	1.34	1.9	2210	0.381	99.95
2.43-2.48	13.77	1.082	2.4	2178	0.3	100
2.48-2.53	13.57	0.838	3.1	2238	0.235	100
2.53-2.59	13.48	0.718	3.7	2168	0.202	100
2.59-2.65	12.73	0.608	4.3	2185	0.177	100
2.65-2.72	13.49	0.476	5.7	2242	0.134	100
2.72-2.81	13.5	0.402	6.9	2158	0.113	100
2.81-2.9	12.8	0.325	8.1	2212	0.094	100
2.9-3	13.43	0.247	11	2228	0.07	100
3-3.12	13.34	0.185	14.8	2200	0.052	99.95
3.12-3.26	12.78	0.149	18.1	2228	0.043	100
3.26-3.43	12.85	0.111	24.1	2223		100	0.032
3.43-3.65	12.61	0.075	34.5	2217	0.022	100
3.65-3.93	12.26	0.059	42	2237	0.018	100
3.93-4.32	12.17	0.047	50.6	2269	0.014	100
4.32-4.95		0.04	57.1	2262	0.012	100
4.95-6.23	12.1	0.039	57	2306	0.012	100
6.23-50	11.39	0.027	69.3	2426	0.008	99.96

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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: 5Y0N

5y0n

Resolution: 2.3→48.906 Å / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 26.7

	R_factor	Num. reflection	% reflection
R_free	0.2254	2225	5 %
R_work	0.2002	-	-
obs	0.2013	44459	99.78 %

Solvent computation

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

Displacement parameters

B_iso max: 184.12 Å² / B_iso mean: 68.71 Å² / B_iso min: 30.83 Å²

Refinement step

Cycle: final / Resolution: 2.3→48.906 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6410	0	62	67	6539
B_iso mean	-	-	69.05	49.3	-
Num. residues	-	-	-	-	802

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	6614
X-RAY DIFFRACTION	f_angle_d	1.252	8950
X-RAY DIFFRACTION	f_chiral_restr	0.045	992
X-RAY DIFFRACTION	f_plane_restr	0.006	1124
X-RAY DIFFRACTION	f_dihedral_angle_d	16.873	2480

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 16

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
2.2996-2.3496	0.4707	137	0.3833	2597	2734	94
2.3496-2.4043	0.3743	135	0.3493	2558	2693	95
2.4043-2.4644	0.3398	137	0.3513	2602	2739	95
2.4644-2.531	0.4143	139	0.3349	2642	2781	95
2.531-2.6055	0.4409	135	0.3145	2568	2703	95
2.6055-2.6896	0.3308	137	0.3009	2601	2738	95
2.6896-2.7857	0.2985	136	0.2801	2586	2722	95
2.7857-2.8973	0.3287	139	0.2954	2636	2775	95
2.8973-3.0291	0.2703	138	0.265	2626	2764	95
3.0291-3.1888	0.2789	138	0.2512	2630	2768	95
3.1888-3.3885	0.2577	139	0.2318	2641	2780	95
3.3885-3.6501	0.2326	138	0.2072	2624	2762	95
3.6501-4.0172	0.1939	142	0.1837	2698	2840	95
4.0172-4.5981	0.1715	140	0.144	2661	2801	95
4.5981-5.7917	0.158	142	0.1463	2698	2840	95
5.7917-48.9153	0.1774	151	0.1432	2851	3002	95

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	1.9709	-0.2472	0.8237	0.8834	-0.0071	0.6369	0.1243	0.2702	-0.0762	-0.4486	-0.0535	-0.0766	-1.0859	-0.6084	0.0443	0.9711	0.2983	0.0388	0.7436	0.0056	0.2132	17.9239	-7.6796	-56.8786
2	7.4277	2.0989	4.6112	3.8804	3.6955	8.2353	0.4737	0.9548	-0.6474	-0.2369	0.361	-0.6388	2.26	0.6013	-0.7854	1.2415	0.0299	-0.0481	0.6364	0.0142	0.4024	45.6862	-2.7919	-63.2899
3	1.0886	-0.0021	0.4275	1.1372	0.9247	5.0175	0.0345	0.0076	0.0623	-0.3844	0.0156	0.0738	-1.2142	-0.5385	-0.0199	0.7056	0.1448	0.0603	0.5575	0.0521	0.2893	20.5908	-5.891	-45.2822
4	1.5907	-0.5284	-1.0751	1.1413	-0.1259	3.1423	-0.192	-0.4972	0.0237	0.3696	0.0903	0.1091	-0.7808	-1.1222	0.1003	0.6401	0.2189	0.0003	0.8424	0.0025	0.2783	24.4411	-1.0803	4.008
5	3.9771	3.8573	3.5438	4.1018	4.6816	7.6054	0.5233	-0.0065	-0.655	0.6384	0.207	-0.5676	0.7231	1.1069	-0.6812	0.6525	0.2244	-0.0359	0.8239	0.0216	0.4983	19.6344	-29.3015	10.5602
6	1.3483	0.0219	0.1424	1.5472	0.507	3.6083	0.0413	-0.1987	0.0387	0.0235	0.0568	0.0932	-0.4558	-0.8644	-0.075	0.4746	0.0819	0.0244	0.678	0.0653	0.2629	22.6258	-3.99	-7.4251

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 1:105)	A	1 - 105
2	X-RAY DIFFRACTION	2	(chain A and resid 106:153)	A	106 - 153
3	X-RAY DIFFRACTION	3	(chain A and resid 154:414)	A	154 - 414
4	X-RAY DIFFRACTION	4	(chain B and resid 1:105)	B	1 - 105
5	X-RAY DIFFRACTION	5	(chain B and resid 106:153)	B	106 - 153
6	X-RAY DIFFRACTION	6	(chain B and resid 154:414)	B	154 - 414

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