PDB-6ajm: Crystal structure of apo AtaTR

ID or keywords:

Entry

Database: PDB / ID: 6ajm

Title

Crystal structure of apo AtaTR

Components

DUF1778 domain-containing protein
N-acetyltransferase

Keywords

TOXIN / antitoxin / acetyltransferase

Function / homology

Function and homology information

toxin sequestering activity / regulation of DNA-templated transcription
Similarity search - Function

Biological species

Escherichia coli (E. coli)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.604 Å

Authors

Yashiro, Y. / Yamashita, S. / Tomita, K.

Funding support

Japan, 2items

Citation

Journal: Structure / Year: 2019
Title: Crystal Structure of the Enterohemorrhagic Escherichia coli AtaT-AtaR Toxin-Antitoxin Complex.
Authors: Yashiro, Y. / Yamashita, S. / Tomita, K.

History

Deposition	Aug 28, 2018	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Jan 2, 2019	Provider: repository / Type: Initial release
Revision 1.1	Jan 23, 2019	Group: Data collection / Database references / Structure summary Category: citation / struct Item: _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI ..._citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.year / _struct.title
Revision 1.2	Feb 13, 2019	Group: Data collection / Database references / Category: citation / Item: _citation.title
Revision 1.3	Mar 20, 2019	Group: Data collection / Database references / Category: citation Item: _citation.journal_volume / _citation.page_first / _citation.year
Revision 1.4	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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Download

PDBx/mmCIF format	6ajm.cif.gz	267.4 KB	Display	PDBx/mmCIF format
PDB format	pdb6ajm.ent.gz	219.3 KB	Display	PDB format
PDBx/mmJSON format	6ajm.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	6ajm_validation.pdf.gz	491.4 KB	Display	wwPDB validaton report
Full document	6ajm_full_validation.pdf.gz	503.2 KB	Display
Data in XML	6ajm_validation.xml.gz	23.2 KB	Display
Data in CIF	6ajm_validation.cif.gz	31.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/aj/6ajm ftp://data.pdbj.org/pub/pdb/validation_reports/aj/6ajm	HTTPS FTP

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Related structure data

Related structure data	6ajnC 5xunS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	6ajn-d 4cxm-d 2pt9-d 4uoe-d 6m5z-d 4cwa-d 3c2g-2 3st7-1 2j0x-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	#146 - Feb 2012 Aminoglycoside Antibiotics similarity (2) #97 - Jan 2008 Circadian Clock Proteins similarity (2)

Deposited unit

A: N-acetyltransferase

B: N-acetyltransferase

C: DUF1778 domain-containing protein

D: DUF1778 domain-containing protein

E: DUF1778 domain-containing protein

F: DUF1778 domain-containing protein

hetero molecules

81.4 kDa, 6 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)	101.090, 116.420, 77.490
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	18
Space group name H-M	P2₁2₁2

#1: Protein	N-acetyltransferase / E.coli ataT Mass: 20772.732 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: BWP17_00640, CVH05_12355 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1V3CQ74
#2: Protein	DUF1778 domain-containing protein / Toxin-antitoxin system / antitoxin component / ribbon-helix-helix fold protein / Ybl13 Mass: 9925.330 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) Gene: ybl13_1, ybl13, A8G17_04185, AA102_09360, AC789_1c38270, ACN002_3543, ACN81_27750, ACU90_15595, AM270_07745, ARC77_13665, AU473_04475, B1K96_23180, B1K96_30445, BHS81_20640, BIZ41_06975, BK292_ ...Gene: ybl13_1, ybl13, A8G17_04185, AA102_09360, AC789_1c38270, ACN002_3543, ACN81_27750, ACU90_15595, AM270_07745, ARC77_13665, AU473_04475, B1K96_23180, B1K96_30445, BHS81_20640, BIZ41_06975, BK292_07330, BMT53_16880, BN17_33961, BTQ04_07040, BWP17_00645, C5P43_28430, C6986_22200, C7B02_13210, C7U73_12315, CHQ87_0001645, COD46_18440, CR538_01655, CVH05_12360, CXB56_05005, ERS085366_00076, ERS085374_01548, ERS085383_01733, ERS085404_01502, RX35_03224 Production host: Escherichia coli (E. coli) / References: UniProt: J7QA90
#3: Chemical	ChemComp-PGE / TRIETHYLENE GLYCOL Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₆H₁₄O₄
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 8 / 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: 2.78 Å³/Da / Density % sol: 55.82 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.6 / Details: 100 mM Tris-HCl pH 8.6, 16% PEG3350, 2% Tacsimate

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

Photon Factory

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

Detector

Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 29, 2017

Radiation

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

Radiation wavelength

Wavelength: 0.98 Å / Relative weight: 1

Reflection

Resolution: 2.6→19.957 Å / Num. obs: 28632 / % possible obs: 99.8 % / Redundancy: 13.108 % / B_iso Wilson estimate: 64.96 Å² / CC_1/2: 0.998 / R_merge(I) obs: 0.141 / R_rim(I) all: 0.147 / Χ²: 1.025 / Net I/σ(I): 13.87

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
2.6-2.67	13.465	2.105	1.34	2057	0.577	2.187	98
2.67-2.74	13.673	1.704	1.75	2015	0.662	1.77	100
2.74-2.82	13.454	1.282	2.36	1988	0.834	1.333	99.9
2.82-2.91	13.086	1.009	2.98	1928	0.861	1.05	100
2.91-3.01	12.693	0.798	3.81	1848	0.91	0.832	100
3.01-3.11	13.277	0.631	4.89	1822	0.951	0.656	100
3.11-3.23	13.722	0.437	6.95	1746	0.986	0.454	99.9
3.23-3.36	13.526	0.349	8.59	1691	0.981	0.363	100
3.36-3.51	13.234	0.241	11.89	1627	0.991	0.25	100
3.51-3.68	12.581	0.184	14.33	1548	0.994	0.192	100
3.68-3.88	13.106	0.136	18.89	1487	0.996	0.141	100
3.88-4.12	13.558	0.107	23.18	1402	0.998	0.111	100
4.12-4.4	13.273	0.083	28.11	1318	0.998	0.087	100
4.4-4.75	12.515	0.073	30.67	1222	0.998	0.077	100
4.75-5.21	12.793	0.076	30.13	1157	0.997	0.079	100
5.21-5.82	13.37	0.083	28.38	1041	0.998	0.086	100
5.82-6.72	12.561	0.076	29.7	928	0.998	0.08	99.9
6.72-8.23	11.936	0.057	35.57	799	0.999	0.059	100
8.23-11.65	12.045	0.047	41.64	639	0.998	0.049	100
11.65-19.957	10.049	0.048	38.18	369	0.998	0.051	97.6

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Processing

Software

Name	Version	Classification
PHENIX	1.12-2829_1309	refinement
XSCALE		data scaling
PDB_EXTRACT	3.24	data extraction
XDS		data reduction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5XUN

5xun

Resolution: 2.604→19.957 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 28.47

	R_factor	Num. reflection	% reflection
R_free	0.2669	1428	5 %
R_work	0.213	-	-
obs	0.2158	28543	99.78 %

Solvent computation

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

Displacement parameters

B_iso max: 229.61 Å² / B_iso mean: 80.8599 Å² / B_iso min: 33.74 Å²

Refinement step

Cycle: final / Resolution: 2.604→19.957 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4946	0	10	8	4964
B_iso mean	-	-	79.96	55.28	-
Num. residues	-	-	-	-	623

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	5029
X-RAY DIFFRACTION	f_angle_d	1.013	6784
X-RAY DIFFRACTION	f_chiral_restr	0.054	773
X-RAY DIFFRACTION	f_plane_restr	0.006	882
X-RAY DIFFRACTION	f_dihedral_angle_d	14.987	3095

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / R_factor R_free error: 0 / Total num. of bins used: 10

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
2.604-2.6969	0.3509	138	0.3008	2630	2768	98
2.6969-2.8046	0.3579	141	0.2809	2663	2804	100
2.8046-2.9318	0.2875	140	0.252	2671	2811	100
2.9318-3.0859	0.3493	143	0.2394	2706	2849	100
3.0859-3.2784	0.2936	141	0.2475	2680	2821	100
3.2784-3.5303	0.2715	143	0.2259	2709	2852	100
3.5303-3.8832	0.2746	142	0.222	2705	2847	100
3.8832-4.4397	0.2341	143	0.1934	2713	2856	100
4.4397-5.5733	0.2784	146	0.1933	2770	2916	100
5.5733-19.958	0.2275	151	0.1907	2868	3019	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	3.0302	0.2215	-1.3165	5.7876	2.7264	7.2327	0.0105	-0.8549	-0.2593	1.0278	0.3846	-0.5349	0.6861	1.2731	-0.4769	0.726	0.0171	-0.1043	0.8124	-0.0315	0.5171	36.6692	61.4319	87.3719
2	0.0809	-0.693	0.4861	4.2722	-4.1805	7.1095	-0.9	0.7295	0.5566	-1.1809	0.5263	1.6706	-1.0077	-1.3813	0.3736	1.557	0.0768	-0.2757	1.031	0.0423	1.1481	16.4033	48.1749	56.2539
3	3.2288	2.3097	2.2414	4.9375	1.4605	7.6102	0.0093	-0.7149	-0.0623	0.6081	-0.2125	0.2471	0.8218	-1.3652	0.1814	0.5214	-0.0474	0.0509	0.7362	-0.038	0.4014	21.1371	59.7469	80.811
4	7.3492	6.736	7.5685	6.2076	6.9853	7.8327	0.5401	1.5539	-1.1527	-0.4675	2.433	-1.0651	3.4689	4.5112	-3.3484	1.1381	0.2711	-0.2075	0.8978	-0.1188	0.7888	36.933	-2.3866	24.9935
5	4.1088	-0.7941	4.1039	5.4765	-2.915	4.9342	0.1949	0.3281	-0.1116	-0.7626	0.1944	-0.6303	-1.204	0.3448	-0.5559	1.0967	0.3667	0.2095	0.867	-0.1448	0.6814	42.1374	9.4888	23.9901
6	7.2755	0.5105	-0.1435	5.631	4.9114	4.8281	0.3616	0.1609	0.1231	-1.0694	0.4507	-0.8959	-0.3147	0.7037	-0.5924	0.6532	0.1109	0.1072	0.4332	-0.0649	0.4624	40.4121	12.9588	30.8088
7	2.4607	-3.0464	-4.5205	5.311	6.5417	8.8444	1.3712	1.1598	-1.7109	-0.7599	2.1009	-2.5841	-0.6583	3.4667	-2.7656	0.9522	0.4224	-0.4542	1.3828	-0.3724	1.2741	43.2218	1.3017	21.5161
8	5.0704	-2.5312	-4.9757	8.645	6.6172	7.152	0.4068	-0.3162	0.4817	0.24	0.7067	-1.0451	0.2581	0.7562	-0.7576	0.418	0.0839	-0.0035	0.4674	0.1643	0.3872	31.7945	12.2172	38.3668
9	4.1053	-5.5107	0.765	7.7549	-1.2079	1.1047	-0.605	0.2963	0.1376	1.0489	0.0783	-0.4817	0.1979	0.221	0.4203	0.379	-0.1854	-0.0607	0.42	-0.0024	0.4466	26.4989	16.4767	47.529
10	6.0105	5.4703	3.6747	5.0654	3.3259	6.097	-0.3541	0.1329	1.4609	-2.7097	-0.6427	1.5385	1.3045	-0.3493	0.5357	1.5395	0.3013	-0.2021	0.8933	0.0932	0.5963	29.4715	9.0063	21.6723
11	5.5567	-2.8491	0.7103	3.6594	1.8233	2.5649	0.0316	0.1371	-0.2008	-0.3049	0.1819	-0.2377	0.5213	-0.5157	-0.0859	0.5993	-0.0642	-0.0377	0.4887	-0.0147	0.379	27.2333	6.238	38.1561
12	6.7473	-3.184	-4.2029	7.5064	3.264	3.1017	0.643	1.1875	-0.0896	-1.1183	0.2001	-0.1432	-0.3407	-0.2487	-0.8967	0.704	0.1269	-0.1281	0.7809	0.0036	0.5306	18.3372	16.3935	33.0722
13	7.8016	-3.4327	-2.0482	9.7969	-4.5348	7.2987	-0.2698	0.0339	-0.7379	0.5738	0.2116	1.5826	0.5164	-0.1494	0.1037	0.3458	-0.1018	-0.067	0.5317	-0.0126	0.387	20.1874	3.7816	41.4711
14	6.6466	3.0267	1.558	7.1155	2.8971	2.6007	0.8072	-0.5404	-0.2177	1.1624	-0.3777	-0.4928	0.6305	0.4564	-0.6062	0.8456	-0.1066	-0.2123	0.5128	0.0521	0.804	54.2803	33.5089	68.4366
15	5.5362	-6.9908	-4.755	8.1832	5.3682	4.3149	-0.0158	-0.1069	-0.1499	0.4136	-0.0039	-0.221	0.2791	-0.1665	-0.0985	0.5786	-0.0729	-0.0292	0.4241	0.0649	0.517	42.5257	42.0293	66.7398
16	9.1476	-5.3427	0.3406	7.7003	4.9105	8.5322	0.2801	-0.4478	-0.5926	0.5487	-0.824	1.9026	0.8746	-2.1306	0.3448	0.6654	-0.302	0.0036	1.1868	0.0719	0.7125	13.4887	53.2103	70.476
17	8.4682	-0.6877	4.5083	5.7358	3.5217	6.9346	-0.1574	-3.0056	1.2126	0.2486	-0.8884	1.3413	-0.2014	-3.0751	0.8244	0.9739	0.4478	0.0766	1.478	-0.2361	0.5517	16.1536	71.2296	86.596
18	7.141	1.1176	-1.5621	6.8152	5.4984	7.7044	0.091	0.5214	0.083	-0.9261	-0.099	-1.2089	-0.8358	0.1111	0.161	0.6418	-0.0756	0.1079	0.5131	0.136	0.7092	52.2818	41.3737	44.1156
19	8.2031	7.4925	6.3593	8.8563	6.4515	5.2295	0.5009	0.5063	-0.1191	0.1607	-0.1153	0.0771	0.5181	-0.218	-0.2807	0.4278	-0.0098	-0.0045	0.4196	-0.0206	0.4171	43.3623	30.1577	47.2963
20	5.9776	-0.8585	-0.6119	6.6765	3.2759	5.6388	0.2808	0.6498	-0.2301	-0.3267	-0.5743	1.1457	0.4645	-0.9987	0.3492	0.5188	-0.0339	-0.189	0.7023	0.0751	0.3537	17.5433	9.0558	40.1786
21	7.0706	-2.0204	1.0637	8.3861	-2.514	9.1829	-0.0486	0.5175	0.8363	0.682	0.04	-1.4574	-0.3379	0.0628	-0.0149	0.6762	-0.0426	-0.2984	0.4726	-0.0934	0.8107	49.7966	45.0201	71.9253
22	3.4667	3.5046	4.3022	2.9299	3.8092	3.472	-0.0137	0.0164	0.3604	1.4776	-0.2908	0.744	1.0554	-0.0027	-0.0123	0.9029	-0.0601	-0.0195	0.4881	0.0689	0.4879	41.7029	21.6968	59.8875
23	5.6161	-4.6518	2.7595	5.4727	-1.3565	6.6225	0.5106	0.7413	-0.7235	-0.6589	-0.2873	0.1529	0.6066	0.1341	-0.2701	0.3644	0.0242	0.1475	0.52	0.0301	0.4761	49.6307	29.3262	39.7604
24	5.1751	-6.0343	-6.9524	4.762	5.8265	6.4177	0.0762	0.2812	-0.2519	-0.6407	-0.5229	0.202	-0.7274	-0.2983	0.0646	0.5253	-0.0071	0.0363	0.4478	-0.0128	0.546	39.2811	50.0838	55.6216

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 through 69 )	A	1 - 69
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 70 through 87 )	A	70 - 87
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 88 through 172 )	A	88 - 172
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 1 through 8 )	B	1 - 8
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 9 through 24 )	B	9 - 24
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 25 through 51 )	B	25 - 51
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 52 through 59 )	B	52 - 59
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 60 through 69 )	B	60 - 69
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 70 through 93 )	B	70 - 93
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 94 through 106 )	B	94 - 106
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 107 through 137 )	B	107 - 137
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 138 through 158 )	B	138 - 158
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 159 through 172 )	B	159 - 172
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 6 through 31 )	C	6 - 31
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 32 through 52 )	C	32 - 52
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 53 through 75 )	C	53 - 75
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 76 through 86 )	C	76 - 86
18	X-RAY DIFFRACTION	18	chain 'D' and (resid 6 through 31 )	D	6 - 31
19	X-RAY DIFFRACTION	19	chain 'D' and (resid 32 through 52 )	D	32 - 52
20	X-RAY DIFFRACTION	20	chain 'D' and (resid 53 through 86 )	D	53 - 86
21	X-RAY DIFFRACTION	21	chain 'E' and (resid 6 through 31 )	E	6 - 31
22	X-RAY DIFFRACTION	22	chain 'E' and (resid 32 through 71 )	E	32 - 71
23	X-RAY DIFFRACTION	23	chain 'F' and (resid 6 through 31 )	F	6 - 31
24	X-RAY DIFFRACTION	24	chain 'F' and (resid 32 through 71 )	F	32 - 71

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