PDB-6rfy: Crystal structure of Eis2 form Mycobacterium abscessus

ID or keywords:

Entry

Database: PDB / ID: 6rfy

Title

Crystal structure of Eis2 form Mycobacterium abscessus

Components

Eis2

Keywords

ANTIBIOTIC / GCN5 N-acetyltransferase / Eis

Function / homology

Function and homology information

N-acetyltransferase activity /

Transferases; Acyltransferases; Transferring groups other than aminoacyl groups
Similarity search - Function

Biological species

Mycobacteroides abscessus (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.2 Å

Authors

Blaise, M. / Kremer, L. / Olieric, V. / Alsarraf, H. / Ung, K.L.

Citation

Journal: Febs J. / Year: 2019
Title: Crystal structure of the aminoglycosides N-acetyltransferase Eis2 from Mycobacterium abscessus.
Authors: Ung, K.L. / Alsarraf, H.M.A.B. / Olieric, V. / Kremer, L. / Blaise, M.

History

Deposition	Apr 16, 2019	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jul 10, 2019	Provider: repository / Type: Initial release
Revision 1.1	Nov 13, 2019	Group: Database references / Category: citation Item: _citation.journal_volume / _citation.page_first / _citation.page_last

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6rfy.cif.gz	952.5 KB	Display	PDBx/mmCIF format
PDB format	pdb6rfy.ent.gz	823.5 KB	Display	PDB format
PDBx/mmJSON format	6rfy.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/rf/6rfy ftp://data.pdbj.org/pub/pdb/validation_reports/rf/6rfy	HTTPS FTP

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Related structure data

Related structure data	6rftC 6rfxC C: citing same article (ref.)
Similar structure data	6rfx-d 6vuu-1 2ozg-1 6vv3-1 6rft-d 6vv0-1 6vv2-1 6vux-1 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 (8) #97 - Jan 2008 Circadian Clock Proteins similarity (1)

Deposited unit

A: Eis2

B: Eis2

C: Eis2

D: Eis2

E: Eis2

F: Eis2

hetero molecules

272 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)	112.690, 79.860, 152.830
Angle α, β, γ (deg.)	90.00, 90.24, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Eis2 Mass: 45121.633 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacteroides abscessus (bacteria) / Gene: D2E36_21790 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: A0A3A1BNP8, UniProt: A0A1M9A4M7*PLUS, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups
#2: Chemical	ChemComp-BTB / 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / BIS-TRIS BUFFER / Bis-tris methane Mass: 209.240 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C₈H₁₉NO₅ / Comment: pH buffer*YM
#3: Chemical	ChemComp-SO4 / SULFATE ION / Sulfate Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO₄
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 986 / 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: 51.58 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 0.2 M Lithium sulfate monohydrate, 0.1 M BIS-TRIS pH 5.5, 25% w/v Polyethylene glycol 3350

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.99 Å
Detector	Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jan 31, 2019
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.99 Å / Relative weight: 1
Reflection	Resolution: 2.2→50 Å / Num. obs: 137957 / % possible obs: 99.9 % / Redundancy: 6.66 % / R_rim(I) all: 0.138 / Net I/σ(I): 10.9
Reflection shell	Resolution: 2.2→2.3 Å / Num. unique obs: 17162 / % possible all: 99.8

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Processing

Software

Name	Version	Classification
PHENIX	(1.15rc3_3435: ???)	refinement
XDS		data reduction
XDS		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.2→49.521 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.28

	R_factor	Num. reflection	% reflection
R_free	0.2302	2005	1.45 %
R_work	0.1994	-	-
obs	0.1999	137910	99.89 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.2→49.521 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	18879	0	100	986	19965

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.002	19374
X-RAY DIFFRACTION	f_angle_d	0.556	26349
X-RAY DIFFRACTION	f_dihedral_angle_d	10.953	11529
X-RAY DIFFRACTION	f_chiral_restr	0.043	2946
X-RAY DIFFRACTION	f_plane_restr	0.004	3422

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 (%)
2.2-2.255	0.4169	141	0.3879	9647	X-RAY DIFFRACTION	100
2.255-2.316	0.4078	142	0.3405	9605	X-RAY DIFFRACTION	100
2.316-2.3841	0.3138	144	0.2961	9657	X-RAY DIFFRACTION	100
2.3841-2.4611	0.341	141	0.2828	9656	X-RAY DIFFRACTION	100
2.4611-2.549	0.2953	143	0.2551	9666	X-RAY DIFFRACTION	100
2.549-2.6511	0.3094	143	0.262	9692	X-RAY DIFFRACTION	100
2.6511-2.7717	0.2966	142	0.246	9657	X-RAY DIFFRACTION	100
2.7717-2.9179	0.303	139	0.2463	9682	X-RAY DIFFRACTION	100
2.9179-3.1007	0.2652	146	0.2295	9703	X-RAY DIFFRACTION	100
3.1007-3.34	0.2382	140	0.2175	9702	X-RAY DIFFRACTION	100
3.34-3.676	0.2239	144	0.1912	9739	X-RAY DIFFRACTION	100
3.676-4.2077	0.1935	144	0.1638	9748	X-RAY DIFFRACTION	100
4.2077-5.3003	0.1663	146	0.1365	9787	X-RAY DIFFRACTION	100
5.3003-49.5337	0.1685	150	0.1527	9964	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	4.0729	0.5469	-1.812	6.247	-1.6598	8.5517	-0.1696	0.347	-0.5608	-0.5283	0.0902	0.0943	0.2984	-0.4613	0.0389	0.3358	-0.0134	-0.0126	0.2845	-0.0419	0.3886	-34.4388	-5.9581	-14.4459
2	6.0931	4.2799	-3.0969	6.0245	-1.1625	3.624	-0.0534	-0.1733	-0.5129	-0.0654	-0.0834	-0.0463	0.4308	-0.3199	0.1425	0.2765	0.0483	0.016	0.2812	0.0521	0.2691	-32.0635	-3.9578	-6.6957
3	7.1452	4.7264	3.2275	4.8608	1.4729	3.5664	-0.0707	0.3697	-0.0883	0.0334	-0.0151	0.2142	-0.129	-0.1408	0.1584	0.25	0.0122	-0.0086	0.245	0.0676	0.1889	-31.0852	5.1819	-5.9459
4	6.3565	2.2605	-3.527	7.1754	0.8188	3.2466	-0.0019	0.3549	0.2894	-0.0725	-0.0178	0.2604	-0.4328	-0.1285	0.0734	0.2846	-0.0399	-0.0564	0.3775	0.065	0.2329	-30.0309	5.8069	-1.6664
5	1.7099	0.2465	-0.1157	2.0455	-0.3526	1.1208	-0.1264	0.2264	-0.2506	-0.2723	-0.0124	-0.5714	0.2428	0.1659	0.1415	0.256	0.0349	0.0745	0.3515	0.0076	0.4447	-9.7805	6.9448	-21.7838
6	3.4442	1.5085	1.3255	3.3682	0.6721	5.3725	-0.083	0.2655	-0.1948	-0.4011	-0.0951	-0.2772	0.0354	-0.0749	0.166	0.3335	0.0514	0.1026	0.2402	0.0449	0.3835	-11.2375	8.6755	-29.1634
7	1.4146	0.4298	-1.3823	0.6328	-1.371	5.897	0.1031	-0.3931	-0.0496	0.3001	-0.1289	-0.2021	-0.2129	0.4754	0.0572	0.38	-0.0513	-0.085	0.3502	0.0536	0.4011	-16.1417	17.1584	1.5889
8	2.1624	-1.5556	-1.4469	4.4779	1.339	2.0381	0.1372	-0.0949	0.1255	0.0567	-0.2058	-0.3719	-0.4212	0.0797	0.0252	0.3578	-0.0432	-0.1047	0.4363	0.0593	0.3244	-17.9852	21.6778	0.0379
9	1.3807	-0.2327	-0.1101	2.2567	-1.0612	3.1965	0.016	-0.0077	0.2039	-0.1173	-0.1662	-0.1099	-0.2373	0.0909	0.1805	0.3496	-0.0718	-0.0728	0.3246	0.0121	0.3624	-5.9414	49.8688	-28.305
10	2.379	0.1475	-0.244	1.9818	-0.5384	0.9116	0.1058	-0.2758	0.0356	0.1839	-0.1586	-0.1359	-0.1106	0.0626	0.0613	0.3029	-0.0623	-0.054	0.3497	0.0026	0.2766	-16.6119	36.8189	-11.8296
11	5.009	1.5049	1.2111	2.241	0.2184	2.8343	-0.2156	-0.2031	0.1237	0.0412	0.0104	-0.0448	-0.3818	0.0356	0.1881	0.3658	0.0855	-0.0309	0.3156	-0.0414	0.3205	-57.6296	48.8918	-18.5667
12	2.1279	0.1448	-0.275	1.9407	0.2606	3.0947	-0.118	0.1569	0.0651	-0.3324	0.1011	0.1045	-0.1211	0.007	0.0229	0.47	0.0103	-0.0664	0.308	0.0194	0.294	-59.1926	40.6096	-46.636
13	1.7884	-0.259	-0.8491	1.1884	-0.1946	2.0607	-0.2305	-0.2566	-0.1698	-0.0627	0.1448	0.4406	0.0751	-0.3463	0.107	0.2752	0.0328	-0.0034	0.5033	0.0184	0.4583	-74.2791	29.61	-23.4564
14	4.2409	-1.1841	-0.7101	1.7801	0.462	1.8827	0.2137	0.0763	-0.1364	-0.4585	-0.0743	-0.0453	0.2215	0.0642	-0.1325	0.9269	-0.1076	-0.1423	0.3271	0.0533	0.3914	-58.1739	-3.7413	-50.9638
15	0.8652	-1.2083	-2.044	3.0616	2.61	8.0117	0.2211	-0.023	-0.0753	-0.6991	-0.1293	0.2212	-0.0984	-0.1917	-0.0535	0.8136	-0.0941	-0.2217	0.4102	0.0229	0.4126	-67.232	4.4744	-52.5703
16	1.6078	-0.5215	0.5662	3.7115	0.2042	1.1707	0.1641	-0.2633	-0.145	0.0777	-0.0318	0.1063	0.3826	-0.1127	-0.1299	0.4657	-0.0568	-0.022	0.4897	0.0396	0.2589	-59.4899	5.9783	-25.2574
17	7.1223	-1.7742	-1.4763	3.9828	1.1776	4.5672	0.096	-0.3426	0.0367	-0.1637	0.0874	-0.1159	0.226	0.1723	-0.1354	0.372	-0.0189	-0.054	0.3059	0.0335	0.2463	-51.9107	8.2603	-23.09
18	3.6892	0.1434	2.7741	1.3588	0.8051	3.7148	0.0866	0.0075	-0.1448	-0.3434	-0.0308	0.4825	0.0607	-0.5226	-0.051	0.4854	-0.0416	-0.1244	0.4289	0.0681	0.4695	-76.808	16.3373	-42.8731
19	1.3895	0.6725	-1.9092	4.7492	1.3241	3.8308	0.0809	0.1903	-0.0019	-0.0387	0.1116	0.7635	-0.1958	-0.4844	-0.1441	0.2982	-0.0582	-0.1032	0.4574	0.0017	0.3575	-75.9219	19.9795	-40.7903
20	4.2669	3.3928	0.5969	5.5429	1.3984	4.4757	-0.1404	-0.476	0.6902	0.0741	-0.0358	0.3048	-0.3338	-0.2711	0.0394	0.5369	0.0486	-0.0393	0.3051	0.0099	0.4395	-40.9829	54.3938	-61.2485
21	8.7956	-1.9327	-0.5746	2.7134	-0.3995	1.3664	0.0955	0.2892	0.8649	-0.1944	-0.0995	0.1699	-0.3484	-0.2527	-0.0667	0.6187	0.0054	-0.1188	0.331	0.0469	0.3973	-40.7134	52.3145	-69.3973
22	5.942	-1.4611	-7.2489	1.2308	1.9485	8.8294	-0.3808	0.1749	-0.0616	-0.0594	0.0019	0.1864	0.0473	-0.1973	0.4381	0.6602	-0.0446	-0.0666	0.3716	0.0986	0.3397	-39.6547	43.2252	-70.1397
23	1.4242	-0.3708	0.1446	1.6428	-0.2361	1.0313	-0.1	0.122	0.1107	-0.2304	0.0048	-0.1455	-0.0526	0.137	0.107	0.5222	-0.0153	0.0199	0.3913	0.0816	0.2609	-23.7773	42.4058	-65.0691
24	3.8556	-0.8201	-0.9975	3.8837	0.2594	4.2361	-0.0423	-0.232	0.0157	0.0757	-0.062	-0.0815	-0.0252	0.2153	0.15	0.4124	-0.0044	-0.0514	0.3401	0.0697	0.2856	-14.6747	40.6619	-52.2926
25	2.3441	-0.7903	1.739	0.3282	-0.2974	5.4588	0.1251	0.4101	0.0043	-0.3875	-0.1537	-0.0163	0.2509	0.0921	0.0406	0.7987	0.0196	0.0221	0.3607	0.068	0.3343	-26.508	31.6632	-80.9818
26	1.2801	0.4243	0.2725	2.3994	0.1028	0.4028	-0.1154	0.2361	-0.1265	-0.4809	0.0492	-0.0949	0.3826	0.1968	0.0335	0.9028	0.0535	0.0369	0.5514	0.0521	0.2968	-27.5447	27.0411	-79.153
27	0.5977	0.3609	0.196	0.5879	0.7103	1.1352	0.1272	-0.047	-0.399	-0.6954	-0.2523	-0.3832	1.4484	0.2614	0.1602	1.366	0.3739	0.2829	0.526	0.0856	0.6571	-10.6851	-5.2535	-51.4644
28	0.8708	0.0959	0.6924	0.0632	-0.2212	2.8565	-0.3207	0.073	0.1206	-0.8623	-0.275	-0.5212	-0.1452	0.6144	0.6509	1.1525	0.2597	0.2428	0.559	0.1417	0.4718	-7.0968	5.0859	-56.2372
29	1.8617	-0.095	-0.3214	0.8419	0.9908	1.2438	-0.0827	-0.2352	-0.6301	-0.7377	-0.3625	-0.7405	0.3671	0.4429	-0.0511	1.1678	0.5176	0.4536	0.662	0.1963	0.7146	-3.8302	5.7396	-59.3723
30	1.931	-1.3806	-0.9014	3.1641	-0.1068	1.2912	0.0641	0.0477	0.0249	-0.5668	-0.0381	0.4771	0.7108	-0.1008	-0.027	0.9486	-0.0128	-0.0739	0.4219	0.0614	0.2828	-37.5089	14.3158	-66.0037
31	1.9657	-0.0412	-0.5901	0.7792	-0.834	1.1005	-0.0701	0.1385	-0.3472	-0.8197	-0.0069	0.0551	0.5734	-0.0709	0.0538	1.3768	0.0142	-0.0301	0.3302	-0.0443	0.471	-32.2359	1.2021	-63.0096
32	4.6335	0.0312	-1.2989	2.1979	-0.4915	3.4332	-0.1411	0.0723	0.0159	-0.609	0.2232	0.2238	0.6018	-0.0826	-0.111	0.894	-0.0093	-0.0424	0.2931	0.0458	0.3571	-37.1471	11.5713	-63.7893
33	0.812	0.2342	0.1101	1.1751	-0.7274	1.0844	-0.1256	0.3491	-0.0461	-1.075	-0.1988	-0.3923	0.751	0.5244	-0.2633	1.2092	0.3208	0.4229	0.7605	0.1149	0.4159	-8.0193	17.4816	-72.517
34	3.1721	0.8291	-0.0916	1.5517	0.9015	2.0699	-0.2073	0.3963	-0.0092	-1.0383	-0.1052	-0.2507	0.5595	0.5961	0.3735	1.0687	0.28	0.2057	0.6244	0.1593	0.4559	-10.493	20.9456	-72.8745

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 2 through 41 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 42 through 68 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 69 through 93 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 94 through 129 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 130 through 199 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 200 through 280 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 281 through 357 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 358 through 411 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 3 through 129 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 130 through 411 )
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 3 through 129 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 130 through 280 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 281 through 411 )
14	X-RAY DIFFRACTION	14	chain 'D' and (resid 3 through 93 )
15	X-RAY DIFFRACTION	15	chain 'D' and (resid 94 through 129 )
16	X-RAY DIFFRACTION	16	chain 'D' and (resid 130 through 199 )
17	X-RAY DIFFRACTION	17	chain 'D' and (resid 200 through 280 )
18	X-RAY DIFFRACTION	18	chain 'D' and (resid 281 through 380 )
19	X-RAY DIFFRACTION	19	chain 'D' and (resid 381 through 411 )
20	X-RAY DIFFRACTION	20	chain 'E' and (resid 3 through 41 )
21	X-RAY DIFFRACTION	21	chain 'E' and (resid 42 through 68 )
22	X-RAY DIFFRACTION	22	chain 'E' and (resid 69 through 93 )
23	X-RAY DIFFRACTION	23	chain 'E' and (resid 94 through 199 )
24	X-RAY DIFFRACTION	24	chain 'E' and (resid 200 through 280 )
25	X-RAY DIFFRACTION	25	chain 'E' and (resid 281 through 357 )
26	X-RAY DIFFRACTION	26	chain 'E' and (resid 358 through 411 )
27	X-RAY DIFFRACTION	27	chain 'F' and (resid 4 through 68 )
28	X-RAY DIFFRACTION	28	chain 'F' and (resid 69 through 93 )
29	X-RAY DIFFRACTION	29	chain 'F' and (resid 94 through 129 )
30	X-RAY DIFFRACTION	30	chain 'F' and (resid 130 through 162 )
31	X-RAY DIFFRACTION	31	chain 'F' and (resid 163 through 240 )
32	X-RAY DIFFRACTION	32	chain 'F' and (resid 241 through 280 )
33	X-RAY DIFFRACTION	33	chain 'F' and (resid 281 through 380 )
34	X-RAY DIFFRACTION	34	chain 'F' and (resid 381 through 411 )

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