PDB-5d6o: Orthorhombic Crystal Structure of an acetylester hydrolase from C...

ID or keywords:

Entry

Database: PDB / ID: 5d6o

Title

Orthorhombic Crystal Structure of an acetylester hydrolase from Corynebacterium glutamicum

Components

Homoserine O-acetyltransferase

Keywords

TRANSFERASE / Acetylester hydrolase / Alpha/Beta Hydrolase

Function / homology

Function and homology information

homoserine O-acetyltransferase activity / Hydrolases; Acting on ester bonds; Carboxylic-ester hydrolases / biosynthetic process / hydrolase activity
Similarity search - Function

Biological species

Corynebacterium glutamicum (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.8 Å

Authors

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

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	Aug 12, 2015	Deposition site: RCSB / Processing site: PDBE
Revision 1.0	Dec 9, 2015	Provider: repository / Type: Initial release
Revision 1.1	Feb 3, 2016	Group: Database references
Revision 1.2	May 1, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5d6o.cif.gz	604.8 KB	Display	PDBx/mmCIF format
PDB format	pdb5d6o.ent.gz	494.7 KB	Display	PDB format
PDBx/mmJSON format	5d6o.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	5d6o_validation.pdf.gz	461.5 KB	Display	wwPDB validaton report
Full document	5d6o_full_validation.pdf.gz	473.7 KB	Display
Data in XML	5d6o_validation.xml.gz	78.1 KB	Display
Data in CIF	5d6o_validation.cif.gz	119.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/d6/5d6o ftp://data.pdbj.org/pub/pdb/validation_reports/d6/5d6o	HTTPS FTP

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Related structure data

Related structure data	5d7bC 5e4yC 5efzC C: citing same article (ref.)
Similar structure data	5efz-1 5efz-3 5efz-2 4xiy-2 1np3-3 3pjq-d 2vat-6 2ah2-d 1s0j-d 2vax-1 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
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

hetero molecules

157 kDa, 4 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 author&software
78.9 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: Homoserine O-acetyltransferase

D: Homoserine O-acetyltransferase

hetero molecules

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

Unit cell

Length a, b, c (Å)	44.141, 89.612, 322.788
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Homoserine O-acetyltransferase Mass: 38870.207 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Corynebacterium glutamicum (strain ATCC 13032 / DSM 20300 / JCM 1318 / LMG 3730 / NCIMB 10025) (bacteria) Strain: ATCC 13032 / DSM 20300 / JCM 1318 / LMG 3730 / NCIMB 10025 Gene: cg0961, Cgl0839 / Plasmid: pHWG771 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 References: UniProt: Q8NS43, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups, homoserine O-acetyltransferase
#2: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cl
#3: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
#4: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: C₃H₈O₃
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 2489 / 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: 2.05 Å³/Da / Density % sol: 40.1 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: Reservoir: 24 %(w/v) PEG4000, 20 %(v/v) glycerol, 0.16 M magnesium chloride, 80 mM Tris/HCl, pH 8.5. Drop before equilibration: 0.4 mikroliter reservoir solution plut 0.8 mikroliter enzyme ...Details: Reservoir: 24 %(w/v) PEG4000, 20 %(v/v) glycerol, 0.16 M magnesium chloride, 80 mM Tris/HCl, pH 8.5. Drop before equilibration: 0.4 mikroliter reservoir solution plut 0.8 mikroliter enzyme solution (protein concentration: 5 mg/ml)

Crystal

Density Matthews: 2.05 Å³/Da / Density % sol: 40.1 %

Crystal grow

Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Reservoir: 24 %(w/v) PEG4000, 20 %(v/v) glycerol, 0.16 M magnesium chloride, 80 mM Tris/HCl, pH 8.5. Drop before equilibration: 0.4 mikroliter reservoir solution plut 0.8 mikroliter enzyme ...

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å
Detector	Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 26, 2008
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.91841 Å / Relative weight: 1
Reflection	Resolution: 1.8→19.93 Å / Num. obs: 120186 / % possible obs: 100 % / Redundancy: 13.1 % / R_sym value: 0.2196 / Net I/σ(I): 12.73
Reflection shell	Resolution: 1.8→1.864 Å / Redundancy: 13.1 % / Mean I/σ(I) obs: 2.28 / % possible all: 100

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Processing

Software

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

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: trigonal structure of the same protein

Resolution: 1.8→19.925 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 18.37 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2103	2370	1.97 %
R_work	0.1746	-	-
obs	0.1754	120181	100 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.8→19.925 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	10968	0	115	2489	13572

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.003	11333
X-RAY DIFFRACTION	f_angle_d	0.719	15373
X-RAY DIFFRACTION	f_dihedral_angle_d	11.153	4042
X-RAY DIFFRACTION	f_chiral_restr	0.029	1640
X-RAY DIFFRACTION	f_plane_restr	0.003	2020

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 (%)
1.8-1.8367	0.2672	142	0.2374	6870	X-RAY DIFFRACTION	100
1.8367-1.8766	0.3071	125	0.2338	6808	X-RAY DIFFRACTION	100
1.8766-1.9202	0.2866	125	0.219	6915	X-RAY DIFFRACTION	100
1.9202-1.9682	0.2631	151	0.2033	6770	X-RAY DIFFRACTION	100
1.9682-2.0214	0.245	132	0.1919	6859	X-RAY DIFFRACTION	100
2.0214-2.0808	0.2216	132	0.1882	6878	X-RAY DIFFRACTION	100
2.0808-2.1479	0.2341	125	0.1765	6812	X-RAY DIFFRACTION	100
2.1479-2.2246	0.2437	128	0.1741	6948	X-RAY DIFFRACTION	100
2.2246-2.3135	0.2298	136	0.1735	6877	X-RAY DIFFRACTION	100
2.3135-2.4186	0.1931	151	0.1746	6875	X-RAY DIFFRACTION	100
2.4186-2.5459	0.2209	149	0.1698	6871	X-RAY DIFFRACTION	100
2.5459-2.7051	0.2196	144	0.1709	6926	X-RAY DIFFRACTION	100
2.7051-2.9133	0.1927	151	0.167	6931	X-RAY DIFFRACTION	100
2.9133-3.2054	0.1774	150	0.1579	6970	X-RAY DIFFRACTION	100
3.2054-3.6667	0.1772	144	0.1493	7015	X-RAY DIFFRACTION	100
3.6667-4.6103	0.1563	136	0.1416	7080	X-RAY DIFFRACTION	100
4.6103-19.926	0.2147	149	0.1889	7406	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	2.3882	-0.8613	0.8922	0.3692	-0.6999	2.8004	0.0035	-0.0811	0.2641	0.2731	-0.0241	0.1014	-0.2557	-0.2368	0.0043	0.1574	0.0028	0.0449	0.1534	-0.0007	0.1193	47.3482	14.212	357.8705
2	0.6078	0.1069	0.233	1.4336	-0.2445	1.1979	0.0093	-0.1637	0.0567	0.0979	0.007	0.0798	-0.0369	0.0811	-0.0143	0.0735	0.0105	0.0124	0.1329	-0.0165	0.0722	57.2891	3.6944	361.7229
3	0.3892	-0.1045	0.1973	0.4636	-0.2361	1.0381	-0.0042	-0.0212	0.0535	0.0738	-0.0011	-0.053	-0.105	0.142	0.0184	0.098	-0.0214	-0.0021	0.134	-0.0013	0.0811	62.0957	8.6617	352.778
4	0.7344	0.4664	-0.0177	0.8936	0.4665	0.8727	0.0152	0.023	0.0427	0.0637	-0.0148	0.1267	0.0129	-0.1558	0.0218	0.0753	0.0321	0.004	0.1098	0.0003	0.0815	44.3901	2.98	337.9247
5	0.5271	-0.0011	-0.1015	0.6115	-0.0993	0.5529	-0.033	-0.0625	-0.0303	-0.0585	0.0292	-0.0667	0.0207	0.1518	0.0007	0.0988	0.0201	-0.01	0.0961	0.0009	0.0611	67.2999	-1.137	346.7173
6	2.2505	0.0827	-0.1466	0.7994	0.1068	1.3514	0.0122	-0.0951	-0.2317	0.0352	-0.0336	0.011	0.3128	-0.0293	-0.0164	0.1542	-0.0079	0.0007	0.0792	0.0101	0.0762	55.8748	-12.2145	351.4528
7	1.9694	-0.4197	1.5455	0.7432	-0.0708	2.9325	0.0262	0.0306	0.1971	-0.2909	-0.0762	-0.0593	-0.3519	0.1156	0.0163	0.1426	0.0026	0.028	0.0806	0.0035	0.098	58.3372	11.5515	302.6799
8	0.8146	-0.3159	0.0435	0.8986	0.1283	1.1954	-0.0087	0.1251	0.0212	-0.0573	-0.0411	0.0413	-0.0538	-0.0194	0.05	0.0806	-0.0024	0.0055	0.0773	-0.009	0.0686	55.6043	-3.0143	301.5239
9	0.4722	-0.034	-0.1102	0.4934	0.2256	0.5275	-0.0113	0.0672	0.0079	-0.0693	-0.0567	0.0726	-0.0651	-0.0933	0.0607	0.0886	0.0264	-0.0066	0.092	-0.0066	0.0756	48.3383	0.3676	309.5025
10	1.5846	-0.6678	0.5869	1.332	-1.0016	1.5509	-0.0072	0.002	0.0774	0.0297	-0.0176	-0.0954	-0.1405	0.1752	0.0269	0.0894	-0.008	0.0049	0.0803	-0.0148	0.0808	65.4951	7.3773	324.3155
11	0.7349	0.1429	0.0436	0.9933	0.0613	0.5584	-0.0266	0.0091	-0.0986	0.0049	0.0173	0.0855	0.0678	-0.1345	0.0231	0.0865	-0.0018	0.0156	0.0977	-0.0196	0.0871	48.4234	-9.365	317.5265
12	1.5184	0.7306	0.1512	1.4981	0.3348	1.3932	0.0035	0.1106	-0.125	0.0315	-0.0023	-0.0985	0.1054	0.1856	0.0109	0.0761	0.0287	0.0036	0.0789	0.0041	0.0851	64.1662	-13.9174	314.5293
13	2.0312	-0.5277	-1.5012	1.2854	0.4787	3.1037	-0.0315	-0.2993	-0.0182	0.1118	-0.0132	-0.0428	0.3466	0.2825	0.0114	0.1292	-0.0142	-0.0108	0.2501	0.0429	0.081	62.9352	-48.3563	424.6328
14	0.8465	0.1114	0.0761	0.8261	-0.1172	1.3732	0.0116	-0.2126	-0.0485	0.1105	-0.0697	-0.0205	-0.0515	0.0938	0.0475	0.1225	-0.0038	-0.0036	0.1423	0.0148	0.0793	52.9606	-37.4311	426.4881
15	0.6484	-0.0227	-0.2959	0.4932	0.1753	1.0825	-0.0033	-0.1089	-0.0863	0.094	-0.0357	0.0395	0.1121	-0.0752	0.0278	0.0839	-0.0118	0.0002	0.1219	0.0171	0.0845	48.1415	-43.9092	418.6231
16	1.1583	0.3532	0.1248	1.1448	-0.0748	0.9414	-0.0878	-0.0663	-0.109	-0.0113	0.101	-0.1157	0.0143	0.133	-0	0.06	0.0061	0.0017	0.1302	-0.0077	0.0785	65.8462	-40.9143	402.9789
17	0.7802	-0.2413	0.0331	0.7246	0.0982	0.5677	0.0071	-0.0131	0.0503	-0.0284	-0.0276	0.019	-0.0595	-0.1893	0.0377	0.0915	0.0049	-0.0032	0.1233	-0.0087	0.0577	42.927	-35.3863	410.9432
18	2.4489	-0.2751	-0.2984	1.4265	0.2871	1.2346	0.0723	-0.04	0.1695	0.0553	-0.0619	-0.1866	-0.2939	0.0238	-0.0844	0.1288	-0.0126	-0.0122	0.0985	-0.0073	0.0735	54.3009	-23.5418	413.6485
19	1.854	0.1542	-1.7826	1.7198	-0.3627	2.711	-0.0611	0.3526	-0.2625	-0.1129	0.0591	0.1412	0.386	-0.2743	0.0036	0.1383	-0.0118	-0.0347	0.1492	-0.0552	0.1544	51.2859	-54.9234	369.5205
20	2.0761	-1.0402	1.4332	1.7318	-1.1545	1.5415	0.0155	0.1612	0.0623	-0.1367	-0.0902	-0.2171	0.1007	0.3645	0.0731	0.1279	-0.0164	0.0243	0.245	-0.047	0.0989	62.5868	-43.7913	362.6419
21	1.2278	-0.6925	0.3377	1.2687	-0.2763	1.1507	-0.036	0.1516	-0.0727	0.018	0.0095	0.0124	0.0321	0.038	0.0184	0.0745	-0.0279	0.0009	0.1002	-0.0209	0.0808	54.5661	-44.4903	370.5083
22	2.1401	-0.3541	0.5467	0.7072	0.3162	1.4596	0.053	0.2617	-0.1629	-0.1519	0.0476	-0.1201	0.0002	0.2083	-0.0716	0.096	-0.0438	0.0111	0.1838	-0.0209	0.0927	62.4067	-38.4455	362.2238
23	0.6374	0.2546	0.097	0.5836	-0.1771	0.7678	-0.0099	0.0894	-0.0463	-0.0121	0.0188	-0.0593	-0.0174	0.1062	0.0104	0.0638	-0.0105	-0.0103	0.1242	-0.0082	0.0864	61.1353	-40.452	380.3459
24	1.5186	-0.7408	-0.1375	2.2252	0.681	0.799	-0.0139	-0.0711	-0.093	0.0175	0.0296	0.1112	0.092	-0.0572	0.001	0.0976	-0.0321	-0.0077	0.0844	0.0018	0.0633	45.7019	-45.6872	391.2831
25	2.5087	-1.7163	-1.0504	1.4315	0.9935	1.7708	-0.1932	0.2787	-0.2031	0.1497	-0.1177	0.2543	0.1234	-0.2646	0.206	0.1086	-0.0342	-0.0062	0.1423	-0.0124	0.1634	42.7012	-50.4297	388.501
26	0.8435	-0.096	-0.0893	0.8312	0.0713	0.4837	-0.0717	-0.0153	0.0541	-0.0551	0.0874	-0.0619	-0.054	0.1652	-0.0099	0.0895	-0.0317	-0.0164	0.1166	-0.0142	0.0789	61.8646	-32.1946	380.8567
27	1.0486	-0.0886	-0.2089	0.9807	-0.1111	1.4725	-0.0578	0.1333	0.1491	-0.0904	-0.0109	0.1705	-0.1447	-0.2068	0.0281	0.1258	-0.01	-0.0393	0.1367	-0.0003	0.0815	46.2133	-27.9847	377.2508

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 1 through 19 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 20 through 81 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 82 through 199 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 200 through 253 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 254 through 310 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 311 through 349 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 1 through 19 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 20 through 81 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 82 through 199 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 200 through 253 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 254 through 310 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 311 through 349 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 1 through 19 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 20 through 81 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 82 through 199 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 200 through 253 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 254 through 310 )
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 311 through 349 )
19	X-RAY DIFFRACTION	19	chain 'D' and (resid 1 through 19 )
20	X-RAY DIFFRACTION	20	chain 'D' and (resid 20 through 50 )
21	X-RAY DIFFRACTION	21	chain 'D' and (resid 51 through 114 )
22	X-RAY DIFFRACTION	22	chain 'D' and (resid 115 through 137 )
23	X-RAY DIFFRACTION	23	chain 'D' and (resid 138 through 199 )
24	X-RAY DIFFRACTION	24	chain 'D' and (resid 200 through 232 )
25	X-RAY DIFFRACTION	25	chain 'D' and (resid 233 through 253 )
26	X-RAY DIFFRACTION	26	chain 'D' and (resid 254 through 310 )
27	X-RAY DIFFRACTION	27	chain 'D' and (resid 311 through 349 )

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