PDB-5efz: Monoclinic structure of the acetyl esterase MekB

ID or keywords:

Entry

Database: PDB / ID: 5efz

Title

Monoclinic structure of the acetyl esterase MekB

Components

Homoserine O-acetyltransferase

Keywords

HYDROLASE / alpha/beta hydrolase / acetyl ester hydrolase / Pseudomonas veronii / transferase

Function / homology

Function and homology information

ethyl acetate hydrolase / biosynthetic process / acyltransferase activity, transferring groups other than amino-acyl groups / hydrolase activity
Similarity search - Function

Biological species

Pseudomonas veronii (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON / Resolution: 1.82 Å

Authors

Toelzer, C. / Pal, S. / Watzlawick, H. / Altenbuchner, J. / Niefind, K.

Citation

Journal: Febs Lett. / Year: 2016
Title: A novel esterase subfamily with alpha / beta-hydrolase fold suggested by structures of two bacterial enzymes homologous to l-homoserine O-acetyl transferases.
Authors: Tolzer, C. / Pal, S. / Watzlawick, H. / Altenbuchner, J. / Niefind, K.

History

Deposition	Oct 26, 2015	Deposition site: RCSB / Processing site: PDBE
Revision 1.0	Dec 16, 2015	Provider: repository / Type: Initial release
Revision 1.1	May 8, 2024	Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	5efz.cif.gz	815 KB	Display	PDBx/mmCIF format
PDB format	pdb5efz.ent.gz	682.4 KB	Display	PDB format
PDBx/mmJSON format	5efz.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ef/5efz ftp://data.pdbj.org/pub/pdb/validation_reports/ef/5efz	HTTPS FTP

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Related structure data

Related structure data	5d6oC 5d7bC 5e4yC C: citing same article (ref.)
Similar structure data	5d6o-1 5d6o-2 1np3-3 4xiy-2 2vat-6 5yu0-1 2ah2-d 3pjq-d 6pkg-d 1n1t-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) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

Related structure data

5d6oC

5d7bC

5e4yC

C: citing same article (ref.)

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#165 - Sep 2013 Designed Protein Cages similarity (2) #216 - Dec 2017 Biodegradable Plastic similarity (1) #220 - Apr 2018 Dehalogenases similarity (2)

Deposited unit

A: Homoserine O-acetyltransferase

B: Homoserine O-acetyltransferase

C: Homoserine O-acetyltransferase

D: Homoserine O-acetyltransferase

E: Homoserine O-acetyltransferase

F: Homoserine O-acetyltransferase

hetero molecules

241 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Homoserine O-acetyltransferase

B: Homoserine O-acetyltransferase

hetero molecules

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

2

C: Homoserine O-acetyltransferase

E: Homoserine O-acetyltransferase

hetero molecules

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

3

D: Homoserine O-acetyltransferase

F: Homoserine O-acetyltransferase

hetero molecules

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

Unit cell

Length a, b, c (Å)	88.848, 110.342, 122.817
Angle α, β, γ (deg.)	90.00, 106.89, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Homoserine O-acetyltransferase / hydrolase Mass: 39746.938 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas veronii (bacteria) / Gene: mekB / Production host: Escherichia coli (E. coli) References: UniProt: Q0MRG5, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups, homoserine O-acetyltransferase
#2: Chemical	... ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 25 / Source method: obtained synthetically / Formula: C₂H₆O₂
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Chemical	ChemComp-ACT / ACETATE ION Mass: 59.044 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C₂H₃O₂
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1085 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION

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Sample preparation

Crystal	Density Matthews: 2.42 Å³/Da / Density % sol: 49.08 %
Crystal grow	Temperature: 293.15 K / Method: vapor diffusion, sitting drop Details: 0.1 M sodium acetate pH 4.5 0.8 M sodium dihydrogen phosphate 1.2 M di-potassium hydrogen phosphate Drop: 0.1 microliter ethylene glycol 0.8 microliter protein solution 0.8 microliter reservoir solution

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
Detector	Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Apr 27, 2015
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 1.82→46.28 Å / Num. obs: 201791 / % possible obs: 99.61 % / Redundancy: 3.5 % / R_sym value: 0.082 / Net I/σ(I): 10.4
Reflection shell	Resolution: 1.82→1.859 Å / Redundancy: 3.4 % / R_merge(I) obs: 0.893 / Mean I/σ(I) obs: 1.4 / % possible all: 98

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Processing

Software

Name	Version	Classification
PHENIX	1.9_1692	refinement
XDS		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Resolution: 1.82→46.28 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.59 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1963	2133	1.06 %
R_work	0.1629	-	-
obs	0.1633	201791	99.61 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 1.82→46.28 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	15939	0	176	1085	17200

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.012	16501
X-RAY DIFFRACTION	f_angle_d	1.217	22302
X-RAY DIFFRACTION	f_dihedral_angle_d	13.679	5922
X-RAY DIFFRACTION	f_chiral_restr	0.061	2395
X-RAY DIFFRACTION	f_plane_restr	0.006	2907

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 (%)
1.82-1.8623	0.3365	151	0.2717	13008	X-RAY DIFFRACTION	98
1.8623-1.9089	0.2909	147	0.2427	13190	X-RAY DIFFRACTION	99
1.9089-1.9605	0.2394	160	0.2141	13258	X-RAY DIFFRACTION	100
1.9605-2.0182	0.2295	155	0.1984	13348	X-RAY DIFFRACTION	100
2.0182-2.0834	0.2074	132	0.181	13303	X-RAY DIFFRACTION	100
2.0834-2.1578	0.2073	140	0.1676	13258	X-RAY DIFFRACTION	100
2.1578-2.2442	0.1947	142	0.1631	13333	X-RAY DIFFRACTION	100
2.2442-2.3464	0.198	125	0.1602	13382	X-RAY DIFFRACTION	100
2.3464-2.47	0.2019	141	0.1587	13291	X-RAY DIFFRACTION	100
2.47-2.6248	0.2108	151	0.1555	13353	X-RAY DIFFRACTION	100
2.6248-2.8274	0.1843	132	0.1578	13323	X-RAY DIFFRACTION	100
2.8274-3.1119	0.1909	140	0.1501	13344	X-RAY DIFFRACTION	100
3.1119-3.5621	0.1767	132	0.1467	13407	X-RAY DIFFRACTION	100
3.5621-4.4872	0.1676	159	0.1387	13352	X-RAY DIFFRACTION	100
4.4872-46.2952	0.188	126	0.1655	13508	X-RAY DIFFRACTION	99

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	3.178	-0.0818	0.6826	1.857	-0.4938	1.4443	0.0251	-0.5054	-0.0411	0.2873	0.0449	0.3244	0.0683	-0.392	-0.0734	0.2068	-0.0815	0.0315	0.348	-0.0062	0.1851	22.1806	93.4241	40.7428
2	5.426	1.7465	0.7009	1.8832	0.2837	0.8612	0.0975	-0.0139	0.3338	-0.0241	-0.083	0.2582	0.0524	-0.292	-0.0044	0.1334	-0.0413	0.0156	0.2666	0.0108	0.1901	15.9314	97.714	25.1692
3	0.9365	0.176	0.2523	0.6944	0.2152	0.6503	0.0385	-0.1258	-0.094	0.0507	-0.0224	0.0112	0.1946	-0.2044	-0.0113	0.1422	-0.0748	-0.0054	0.1945	0.0332	0.1839	27.163	88.968	31.3102
4	1.2988	-0.235	1.0286	2.101	-2.0035	5.8332	-0.0607	-0.0691	0.2813	0.2318	-0.0164	-0.2263	-0.5709	0.2429	0.0845	0.1362	-0.0363	0.0081	0.1522	-0.0306	0.2374	40.923	109.4725	31.1271
5	2.7088	0.5574	-0.7014	2.3127	0.523	4.1845	0.1438	-0.2429	0.1925	0.213	-0.0718	0.0851	-0.1875	-0.1198	-0.0662	0.0809	-0.0336	-0.0053	0.1842	-0.0169	0.1646	35.3675	102.5726	36.2695
6	1.6749	-0.3825	1.2999	1.4611	0.1936	2.3418	0.0807	0.032	-0.2214	0.0383	-0.0405	-0.0694	0.3087	-0.0746	-0.0333	0.1375	-0.0364	0.0192	0.1461	-0.0205	0.1955	33.5746	86.3685	20.0909
7	1.6895	-0.2879	0.7124	5.4024	1.6176	3.522	0.0294	0.2108	-0.1548	-0.4991	0.0097	0.1269	0.2213	-0.1545	-0.0372	0.1314	-0.055	0.0289	0.2332	0.0076	0.1515	31.1345	90.6032	11.5781
8	4.027	3.4624	0.559	4.744	0.6717	1.2305	-0.0717	0.1914	0.0229	-0.1852	0.0659	0.1116	-0.0201	-0.273	-0.0046	0.1049	-0.0086	0.0139	0.2444	0.0363	0.1585	22.5247	98.5708	14.7044
9	1.5855	0.3141	-0.8107	1.3573	-0.6903	1.9614	-0.0251	0.2094	0.0329	-0.0414	0.0062	-0.2344	0.0298	0.3303	0.032	0.1326	-0.0433	0.0467	0.3073	-0.0363	0.2779	75.0969	108.4283	13.1208
10	1.1694	0.1222	0.103	1.1329	-0.0521	0.9394	-0.0246	0.1873	0.2712	-0.0934	0.0413	-0.0554	-0.1964	0.2268	-0.0285	0.1834	-0.0749	0.0491	0.2056	0.0095	0.2378	66.5508	115.2424	14.4061
11	1.3686	1.7865	1.1449	5.5202	3.5821	4.2097	0.1248	-0.1239	-0.1039	0.3592	-0.0497	-0.0633	0.2718	0.0021	-0.0799	0.104	-0.019	0.0307	0.1178	0.0136	0.1479	57.0166	96.9529	28.1273
12	1.9905	-0.2075	0.9526	1.158	-0.586	3.376	-0.028	0.0697	0.2711	0.0456	0.0184	0.0397	-0.4023	0.1254	0.0178	0.1364	-0.0402	0.0508	0.1228	-0.0133	0.2062	60.0789	112.967	19.4306
13	2.5754	0.0255	-0.7218	3.6058	-1.3522	3.238	-0.0174	0.4005	0.0426	-0.279	0.0513	0.0528	-0.0788	0.041	-0.0391	0.1488	-0.0415	0.0029	0.1859	-0.0212	0.1312	56.467	104.2264	3.9435
14	5.7189	-2.127	-5.0998	0.8596	2.1379	6.9893	-0.1078	0.2455	0.2265	-0.26	0.0565	-0.0104	-0.3277	-0.2219	0.0474	0.3838	-0.0211	-0.0625	0.1613	0.016	0.2747	79.1123	81.087	45.0769
15	1.677	-0.0836	0.2336	1.9904	1.2374	2.8273	-0.1881	-0.2651	0.0423	0.2383	0.1418	0.0989	-0.2103	-0.1032	0.055	0.2765	0.0624	-0.0249	0.1633	-0.0011	0.201	78.2275	76.3383	60.1798
16	1.8077	0.2925	0.7929	1.6607	0.566	2.4988	-0.1159	0.0608	0.0818	-0.0144	0.0458	-0.0863	-0.2064	0.1254	0.0574	0.1487	-0.0149	0.0144	0.1285	0.0145	0.1474	85.7376	71.3825	49.2473
17	1.4913	-0.4856	1.4741	2.0632	-2.537	6.1393	-0.0922	-0.2405	-0.4462	0.0954	0.2638	0.3398	0.4372	-0.4718	-0.1842	0.281	0.0081	0.0958	0.1729	0.0412	0.324	75.0319	51.4672	55.1791
18	5.1267	0.2364	1.4026	2.0039	0.135	2.7059	-0.1554	0.145	0.2592	-0.1661	0.0505	-0.3469	-0.1893	0.5658	0.1004	0.1715	-0.0425	0.0283	0.2149	0.0147	0.2151	92.7738	69.5595	46.9539
19	2.5079	0.2116	-0.762	1.9731	-0.3581	2.3738	-0.2055	-0.3281	-0.1134	0.2695	0.125	-0.252	0.0901	0.4541	0.072	0.2424	0.104	-0.037	0.2727	0.0115	0.1864	91.9778	64.2403	65.6827
20	0.3365	0.0034	0.1661	0.3028	-0.0874	0.3967	0.213	-0.25	-0.2878	-0.1163	0.2093	0.3215	1.0661	-0.8419	-0.0397	0.7367	-0.4982	-0.1045	0.4085	0.3623	0.247	42.2069	40.4446	25.5679
21	2.4849	0.2795	0.7566	1.5811	-0.0473	2.5279	0.0861	0.0374	-0.3205	-0.358	0.0594	-0.0518	0.6264	0.1421	-0.1298	0.4055	0.0275	-0.0056	0.1594	0.0433	0.1716	56.3724	47.3321	12.9923
22	2.659	-0.0206	-0.7398	3.0482	-1.1755	3.5188	0.0531	-0.418	-0.0374	0.2542	0.0122	-0.0374	0.3117	0.0448	-0.0293	0.2388	-0.0171	-0.0331	0.2194	0.023	0.1168	55.015	50.4632	34.8917
23	0.7343	-0.6837	-0.4772	1.7396	0.1067	0.4197	0.1561	0.4335	-0.3328	-0.426	-0.0826	-0.0482	0.4374	0.0288	-0.0543	0.7525	0.2207	-0.2355	0.5162	-0.2354	0.4966	88.8767	19.7995	38.7853
24	2.9831	-1.3713	-0.2144	3.3341	0.2437	0.0261	0.164	0.0409	-0.2836	-0.2734	0.0114	-0.4089	0.408	0.4354	-0.1428	0.6488	0.2548	-0.0921	0.4358	-0.1262	0.396	102.8847	22.0262	48.4842
25	0.7566	0.0449	-0.5357	1.3869	0.361	0.4921	0.3192	0.2327	-0.374	-0.1822	-0.121	0.1702	0.3777	-0.0292	-0.1514	0.5245	0.0957	-0.1639	0.2459	-0.0672	0.3552	87.6779	24.2104	49.8492
26	2.5862	-1.5176	1.4936	3.5776	-2.0519	1.3765	0.1822	0.2168	-0.0306	-0.2646	-0.0248	0.1326	0.0938	-0.0256	-0.1076	0.9323	0.4898	0.0276	0.7384	0.1204	0.3968	78.845	39.926	31.256
27	4.9236	1.2575	2.6315	2.0989	1.5881	3.8693	0.2131	0.7292	0.5887	-0.7483	-0.0755	-0.3268	-0.5503	0.467	-0.1322	0.6403	0.1283	0.2483	0.3519	0.0564	0.4263	96.8213	49.1582	42.8461
28	2.026	1.5672	0.966	3.2208	0.3788	2.5068	0.332	0.7161	-0.026	-0.6955	0.0116	-0.197	0.0044	0.1182	-0.3225	0.5312	0.2351	0.0204	0.3698	-0.0278	0.2617	88.0699	36.4375	38.4735
29	3.3903	1.0239	-0.6509	1.9812	-0.5027	5.3064	0.1189	-0.1414	-0.4769	-0.4301	0.018	0.1079	0.6954	-0.4169	-0.1168	0.4007	-0.0466	-0.0908	0.2045	0.0106	0.3347	80.9122	27.4022	61.0715
30	3.6094	-0.3734	-0.8352	2.8778	-0.7642	3.1141	0.2522	-0.2212	0.0466	-0.0993	0.0356	-0.2436	0.2595	0.488	-0.2687	0.2704	0.0513	-0.0588	0.2488	-0.1035	0.2205	99.1603	33.9405	60.1891
31	1.4517	0.6834	0.1265	1.2076	-0.0847	0.9079	-0.0188	0.1927	0.064	-0.1031	-0.0059	-0.0749	-0.0615	0.2747	0.0199	0.0985	-0.0185	0.0195	0.2398	-0.0035	0.1474	81.4697	73.1884	5.2854
32	1.674	-0.3834	-1.268	1.4745	2.3768	6.5303	-0.0167	0.2056	-0.0101	-0.0479	-0.1206	0.2583	0.0868	-0.3597	0.13	0.0964	-0.0319	-0.0101	0.096	-0.0037	0.1797	58.0665	65.3986	7.3815
33	2.0603	0.4887	1.0778	1.0561	-0.2906	2.1507	0.0314	0.1852	-0.2087	-0.1086	0.0326	0.0122	0.1484	0.3226	-0.0525	0.1186	0.0054	0.0317	0.1874	-0.0401	0.1219	76.2044	62.6581	6.8755
34	2.8446	0.4619	0.1131	1.8982	-0.1557	0.9329	0.0355	-0.1733	0.027	0.1296	-0.0602	-0.0324	-0.0409	0.2314	0.024	0.1304	-0.0421	0.0203	0.2123	-0.0161	0.1103	77.9112	70.6093	23.4919

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 3 through 40 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 41 through 80 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 81 through 180 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 181 through 240 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 241 through 260 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 261 through 300 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 301 through 320 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 321 through 349 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 3 through 80 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 81 through 180 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 181 through 240 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 241 through 280 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 281 through 347 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 10 through 32 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 33 through 99 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 100 through 197 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 198 through 250 )
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 251 through 280 )
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 281 through 348 )
20	X-RAY DIFFRACTION	20	chain 'D' and (resid 2 through 175 )
21	X-RAY DIFFRACTION	21	chain 'D' and (resid 176 through 275 )
22	X-RAY DIFFRACTION	22	chain 'D' and (resid 276 through 346 )
23	X-RAY DIFFRACTION	23	chain 'E' and (resid 3 through 40 )
24	X-RAY DIFFRACTION	24	chain 'E' and (resid 41 through 80 )
25	X-RAY DIFFRACTION	25	chain 'E' and (resid 81 through 180 )
26	X-RAY DIFFRACTION	26	chain 'E' and (resid 181 through 200 )
27	X-RAY DIFFRACTION	27	chain 'E' and (resid 201 through 240 )
28	X-RAY DIFFRACTION	28	chain 'E' and (resid 241 through 260 )
29	X-RAY DIFFRACTION	29	chain 'E' and (resid 261 through 280 )
30	X-RAY DIFFRACTION	30	chain 'E' and (resid 281 through 347 )
31	X-RAY DIFFRACTION	31	chain 'F' and (resid 3 through 180 )
32	X-RAY DIFFRACTION	32	chain 'F' and (resid 181 through 240 )
33	X-RAY DIFFRACTION	33	chain 'F' and (resid 241 through 280 )
34	X-RAY DIFFRACTION	34	chain 'F' and (resid 281 through 349 )

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