PDB-5kl9: Crystal structure of a putative acyl-CoA thioesterase EC709/ECK07...

ID or keywords:

Entry

Database: PDB / ID: 5kl9

Title

Crystal structure of a putative acyl-CoA thioesterase EC709/ECK0725 from Escherichia coli in complex with CoA

Components

Acyl-CoA thioester hydrolase YbgC

Keywords

HYDROLASE / alpha/beta fold / hotdog fold / acyl-CoA / thioesterase / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID

Function / homology

Function and homology information

thiolester hydrolase activity / fatty acyl-CoA hydrolase activity / Hydrolases; Acting on ester bonds; Thioester hydrolases / lipid metabolic process / plasma membrane
Similarity search - Function

Biological species

Escherichia coli O157:H7 (bacteria)

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT / Resolution: 2.22 Å

Authors

Stogios, P.J. / Skarina, T. / Di Leo, R. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)

Citation

Journal: To Be Published
Title: Crystal structure of a putative acyl-CoA thioesterase EC709/ECK0725 from Escherichia coli in complex with CoA
Authors: Stogios, P.J.

History

Deposition	Jun 23, 2016	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jul 6, 2016	Provider: repository / Type: Initial release
Revision 1.1	Aug 24, 2016	Group: Other
Revision 1.2	Aug 31, 2016	Group: Database references
Revision 1.3	Nov 22, 2017	Group: Derived calculations / Refinement description / Category: pdbx_struct_oper_list / software Item: _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 1.4	Sep 27, 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	5kl9.cif.gz	239.8 KB	Display	PDBx/mmCIF format
PDB format	pdb5kl9.ent.gz	194.1 KB	Display	PDB format
PDBx/mmJSON format	5kl9.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	5kl9_validation.pdf.gz	976.4 KB	Display	wwPDB validaton report
Full document	5kl9_full_validation.pdf.gz	988.5 KB	Display
Data in XML	5kl9_validation.xml.gz	27.1 KB	Display
Data in CIF	5kl9_validation.cif.gz	37.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/kl/5kl9 ftp://data.pdbj.org/pub/pdb/validation_reports/kl/5kl9	HTTPS FTP

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Related structure data

Related structure data	1s5uS S: Starting model for refinement
Similar structure data	5t06-d 5t07-d 2xfl-2 2egj-1 4jx1-4 4jx1-1 3bwg-1 2xem-d 2oaf-1 4e16-1 Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search
Other databases	TargetTrack: CSGID-IDP95663

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#90 - Jun 2007 Fatty Acid Synthase similarity (1) #146 - Feb 2012 Aminoglycoside Antibiotics similarity (1) #93 - Sep 2007 Citrate Synthase similarity (1) #154 - Oct 2012 Citric Acid Cycle similarity (1) #216 - Dec 2017 Biodegradable Plastic similarity (1) #39 - Mar 2003 lac Repressor similarity (1)

Deposited unit

A: Acyl-CoA thioester hydrolase YbgC

B: Acyl-CoA thioester hydrolase YbgC

C: Acyl-CoA thioester hydrolase YbgC

D: Acyl-CoA thioester hydrolase YbgC

hetero molecules

64.6 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	63.702, 97.195, 96.114
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Acyl-CoA thioester hydrolase YbgC / Acyl-CoA thioesterase Mass: 15581.996 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli O157:H7 (bacteria) / Gene: ybgC, Z0904, ECs0771 / Plasmid: pMCSG68SBPTEV / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: P0A8Z5, UniProt: P0A8Z3*PLUS, Hydrolases; Acting on ester bonds; Thioester hydrolases
#2: Chemical	ChemComp-COA / COENZYME A Mass: 767.534 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂₁H₃₆N₇O₁₆P₃S
#3: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO₄
#4: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₃H₈O₃
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 350 / 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: 2.39 Å³/Da / Density % sol: 48.47 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 2 M ammonium sulfate, 1% PEG200, 2.5 mM hexanoyl-CoA

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
Detector	Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Apr 22, 2016
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.5418 Å / Relative weight: 1
Reflection	Resolution: 2.22→30 Å / Num. obs: 29725 / % possible obs: 98.7 % / Redundancy: 3.4 % / R_merge(I) obs: 0.088 / Net I/σ(I): 19.76
Reflection shell	Resolution: 2.22→2.26 Å / Redundancy: 3.3 % / R_merge(I) obs: 0.709 / Mean I/σ(I) obs: 2.18 / % possible all: 99.2

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Processing

Software

Name	Version	Classification
PHENIX	1.9_1692	refinement
HKL-3000		data reduction
HKL-3000		data scaling
PHENIX		phasing
Coot		model building

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1S5U

1s5u

Resolution: 2.22→28.878 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 25.66

	R_factor	Num. reflection	% reflection
R_free	0.2394	1483	5 %
R_work	0.1928	-	-
obs	0.1951	29684	98.28 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.22→28.878 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4254	0	139	350	4743

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.005	4488
X-RAY DIFFRACTION	f_angle_d	0.906	6099
X-RAY DIFFRACTION	f_dihedral_angle_d	15.359	1674
X-RAY DIFFRACTION	f_chiral_restr	0.036	682
X-RAY DIFFRACTION	f_plane_restr	0.003	756

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 (%)
2.22-2.2904	0.3331	125	0.264	2433	X-RAY DIFFRACTION	95
2.2904-2.3722	0.2819	134	0.2574	2560	X-RAY DIFFRACTION	100
2.3722-2.4671	0.3091	140	0.2429	2569	X-RAY DIFFRACTION	100
2.4671-2.5793	0.3413	132	0.2373	2555	X-RAY DIFFRACTION	100
2.5793-2.7152	0.305	136	0.2183	2566	X-RAY DIFFRACTION	100
2.7152-2.8852	0.2744	136	0.2221	2591	X-RAY DIFFRACTION	100
2.8852-3.1077	0.2976	132	0.2119	2582	X-RAY DIFFRACTION	99
3.1077-3.42	0.2565	139	0.2012	2558	X-RAY DIFFRACTION	99
3.42-3.9139	0.2233	131	0.167	2553	X-RAY DIFFRACTION	98
3.9139-4.9271	0.1552	134	0.1405	2594	X-RAY DIFFRACTION	97
4.9271-28.8805	0.2153	144	0.1908	2640	X-RAY DIFFRACTION	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	3.6703	-1.6637	0.7528	6.2707	-0.3832	2.797	0.0139	0.0765	-0.0852	0.0282	0.0959	-0.2174	0.0067	0.0442	-0.1271	0.2234	-0.0288	0.0119	0.2191	-0.0076	0.1844	23.4223	-5.9077	-5.0621
2	2.6472	3.2449	1.1689	4.3061	0.9884	1.1755	0.447	0.2691	-0.1213	1.3915	0.4995	1.3399	-0.2395	-0.3178	-0.8765	0.6546	0.088	-0.036	0.5199	0.0933	0.4725	30.2239	-16.3036	12.8766
3	2.1148	-0.8746	0.3587	2.0889	0.3907	3.3612	-0.0451	0.0224	0.1394	-0.2978	0.12	-0.0726	-0.1594	-0.0802	-0.0663	0.3038	-0.0546	0.0221	0.2637	0.0409	0.2706	26.1063	1.2136	-5.2032
4	5.809	-1.9473	4.6932	6.8678	-4.506	7.4923	-0.0586	0.1564	0.1649	0.1719	0.024	-0.1444	-0.1596	0.5215	0.1074	0.207	-0.0014	0.0355	0.2408	-0.0453	0.2371	30.4412	-0.3454	-2.1603
5	2.6347	-4.0152	-1.2204	7.6658	4.3451	8.0684	-0.0185	-0.3027	0.1852	0.4111	0.3242	-0.5929	1.0514	0.0746	-0.4965	0.3386	0.0619	-0.0361	0.4033	-0.0632	0.4016	38.9251	-10.5992	7.2063
6	2.6272	-0.055	2.2467	1.2152	0.0097	6.5019	0.0434	0.0514	0.0927	-0.0116	0.0101	0.149	0.0341	-0.1907	-0.0572	0.1969	-0.0106	0.0166	0.2201	0.0221	0.2568	10.0792	-13.3303	-6.7346
7	4.9815	-1.4373	0.1222	4.7631	-2.6241	7.3928	0.2054	0.2741	0.2234	-0.2811	0.3281	0.3109	-0.558	-0.7642	-0.6018	0.3561	-0.0017	0.0435	0.2684	-0.0708	0.2807	-0.6715	-10.2434	-8.5796
8	7.4699	-2.8887	3.9233	3.9427	-1.3532	4.3322	0.0164	-0.0427	-0.6523	-0.2032	0.0831	0.332	0.255	-0.4257	-0.1236	0.2317	-0.0615	0.0175	0.3003	0.0106	0.2178	4.8045	-19.4335	-7.3375
9	8.6351	-3.4016	5.1105	5.9789	-5.005	4.8908	0.9912	0.4047	-1.2574	-0.6583	-0.3673	1.0519	0.535	-0.1535	-0.1263	0.368	-0.0272	0.0184	0.4396	-0.0351	0.241	2.0288	-18.9689	-4.737
10	8.6737	-2.6848	-2.8739	4.9143	-0.5425	8.4122	0.3659	0.4158	0.9727	-0.4775	-0.5826	0.5497	-2.3752	-1.2885	0.2285	0.8106	0.098	-0.0723	0.73	-0.0111	0.5411	-8.6576	-3.6248	-17.5835
11	4.2617	-5.1076	-2.108	6.2321	2.9806	2.8675	-0.9058	0.2767	-2.6989	0.1605	-0.0607	1.7801	0.9095	-1.0794	0.9851	0.5601	-0.1542	0.0097	0.9914	-0.06	0.6671	-3.846	-18.2432	-23.0006
12	1.0199	0.5133	1.4133	3.6541	-2.8713	5.5138	0.0549	-0.0268	0.2297	0.0797	0.1477	0.2596	-0.1922	-0.1502	-0.1718	0.1902	0.0501	0.0274	0.2885	-0.0385	0.2979	0.9129	-1.3244	10.0382
13	4.2646	-1.6024	0.4302	1.1278	-2.0098	6.4515	-0.5829	0.8005	0.2798	-0.1737	-0.1325	-0.117	-0.5278	0.7903	-2.9125	1.9297	-0.0853	-0.6324	0.7616	-0.1701	0.2753	10.4618	-11.8933	23.7694
14	1.9451	-1.6686	-1.5127	8.1347	0.2756	2.9145	-0.2241	-0.0505	0.0363	0.4569	0.2246	0.0752	-0.0252	-0.1428	0.0197	0.2496	0.0301	0.0112	0.3777	-0.0289	0.2722	-1.8699	-6.0566	7.2766
15	4.8667	-0.373	1.4183	4.3431	-5.2733	6.721	-0.0538	-0.0683	-0.0025	0.8662	-0.0818	0.4762	0.8657	-0.263	0.1028	0.5953	-0.0274	0.1245	0.5931	-0.0228	0.3346	-5.738	-16.5091	17.5747
16	7.6769	-4.7414	3.2885	4.3724	-3.9082	8.5829	-0.3482	-0.3002	0.1542	0.6658	0.3114	-0.0726	0.3255	-0.6442	-0.0135	0.3563	-0.0297	-0.0097	0.3833	-0.0959	0.2662	-5.7531	-7.146	9.3
17	7.7384	2.5351	6.5817	7.6007	0.5955	5.9735	0.0427	-0.7251	-0.4247	1.2032	0.538	-0.8195	0.1961	1.5658	-0.552	1.36	0.0059	-0.0213	0.7632	-0.0017	0.5267	4.1935	-20.5198	23.0205
18	2.5239	-0.8016	0.2244	4.5849	-1.1131	4.6853	-0.0305	-0.1174	0.1943	0.228	0.0394	0.1787	-0.1494	-0.3348	-0.0002	0.2321	-0.0065	-0.0003	0.3089	-0.0633	0.2652	13.1081	6.041	10.5776
19	8.29	3.3442	-2.7977	6.6616	1.4021	3.6399	0.1596	0.1056	0.0207	0.8411	1.7464	1.533	0.4797	-0.2309	-1.6922	1.1058	0.2759	-0.0381	0.6476	0.1019	1.0731	3.3686	19.1632	-1.5716
20	2.6983	-0.3822	-0.9239	3.778	-1.6408	5.4758	0.2601	0.039	0.5813	-0.1462	-0.0411	0.0516	-0.3991	-0.1031	-0.1758	0.2964	0.0098	0.0105	0.2157	-0.0418	0.3072	19.4322	12.347	8.2005
21	3.0147	-2.9038	1.969	7.7926	-5.4826	3.9144	0.2955	0.0837	0.3648	0.0824	-0.3077	-0.2386	-0.3901	0.5994	0.053	0.2175	-0.0798	0.0751	0.3528	-0.057	0.3749	20.5519	11.4492	11.051
22	3.4914	3.3197	-1.7416	5.8146	2.7036	8.02	0.2264	1.1724	0.047	-0.315	0.3817	0.4546	1.8429	-2.2204	-0.6303	1.659	0.1427	-0.2246	1.1485	-0.0835	0.822	11.0208	18.8	-12.6866
23	3.3095	-3.3255	-1.4794	3.3829	1.524	0.7221	0.1488	-0.2246	1.3027	0.8943	0.4834	0.5909	-1.0337	-0.5623	0.0585	1.28	0.3562	0.4559	0.4247	0.2524	1.179	10.0774	28.355	1.6902

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(chain A and resid 1:50)
2	X-RAY DIFFRACTION	2	(chain A and resid 51:55)
3	X-RAY DIFFRACTION	3	(chain A and resid 56:85)
4	X-RAY DIFFRACTION	4	(chain A and resid 86:117)
5	X-RAY DIFFRACTION	5	(chain A and resid 118:134)
6	X-RAY DIFFRACTION	6	(chain B and resid 4:47)
7	X-RAY DIFFRACTION	7	(chain B and resid 48:69)
8	X-RAY DIFFRACTION	8	(chain B and resid 70:99)
9	X-RAY DIFFRACTION	9	(chain B and resid 100:114)
10	X-RAY DIFFRACTION	10	(chain B and resid 115:128)
11	X-RAY DIFFRACTION	11	(chain B and resid 129:133)
12	X-RAY DIFFRACTION	12	(chain C and resid 4:44)
13	X-RAY DIFFRACTION	13	(chain C and resid 45:53)
14	X-RAY DIFFRACTION	14	(chain C and resid 54:79)
15	X-RAY DIFFRACTION	15	(chain C and resid 80:93)
16	X-RAY DIFFRACTION	16	(chain C and resid 94:115)
17	X-RAY DIFFRACTION	17	(chain C and resid 116:132)
18	X-RAY DIFFRACTION	18	(chain D and resid 4:42)
19	X-RAY DIFFRACTION	19	(chain D and resid 43:55)
20	X-RAY DIFFRACTION	20	(chain D and resid 56:96)
21	X-RAY DIFFRACTION	21	(chain D and resid 97:114)
22	X-RAY DIFFRACTION	22	(chain D and resid 115:123)
23	X-RAY DIFFRACTION	23	(chain D and resid 124:132)

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