PDB-7lcl: Zoogloea ramigera biosynthetic thiolase Q183Y mutant

ID or keywords:

Entry

Database: PDB / ID: 7lcl

Title

Zoogloea ramigera biosynthetic thiolase Q183Y mutant

Components

Acetyl-CoA acetyltransferase

Keywords

TRANSFERASE /

acetyl-CoA C-acetyltransferase /

acetoacetyl-CoA thiolase / type II thiolase / biosynthetic thiolase / potassium activation

Function / homology

Function and homology information

poly-hydroxybutyrate biosynthetic process /

acetyl-CoA C-acetyltransferase /

acetyl-CoA C-acetyltransferase activity /

cytoplasm
Similarity search - Function

Biological species

Zoogloea ramigera (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 2.295 Å

Authors

Marshall, A.C. / Bruning, J.B.

Citation

Journal: Biochem.J. / Year: 2021
Title: Engineering potassium activation into biosynthetic thiolase.
Authors: Marshall, A.C. / Bruning, J.B.

History

Deposition	Jan 11, 2021	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Sep 1, 2021	Provider: repository / Type: Initial release
Revision 1.1	Oct 18, 2023	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	7lcl.cif.gz	595.9 KB	Display	PDBx/mmCIF format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/lc/7lcl ftp://data.pdbj.org/pub/pdb/validation_reports/lc/7lcl	HTTPS FTP

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Related structure data

Related structure data	7lbzC 7lcaC 7ld2C 7ldcC 7ldtC 7lduC 7ldvC 7ldwC 1qflS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	1qfl-d 7ldc-d 1nl7-d 7ldu-d 1m1o-d 7lbz-d 2wkv-d 2vtz-d 7ldv-d 7lca-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	#216 - Dec 2017 Biodegradable Plastic similarity (14) #135 - Mar 2011 Integrase similarity (1) #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) #39 - Mar 2003 lac Repressor similarity (1)

Deposited unit

A: Acetyl-CoA acetyltransferase

B: Acetyl-CoA acetyltransferase

C: Acetyl-CoA acetyltransferase

D: Acetyl-CoA acetyltransferase

hetero molecules

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

1

Idetical with deposited unit
defined by author&software
Evidence: homology

Unit cell

Length a, b, c (Å)	84.175, 79.071, 149.635
Angle α, β, γ (deg.)	90.000, 93.780, 90.000
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Acetyl-CoA acetyltransferase / Acetoacetyl-CoA thiolase / Beta-ketothiolase Mass: 41578.367 Da / Num. of mol.: 4 / Mutation: Q183Y Source method: isolated from a genetically manipulated source Source: (gene. exp.) Zoogloea ramigera (bacteria) / Gene: phaA, phbA / Plasmid: pET11a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P07097, acetyl-CoA C-acetyltransferase
#2: Chemical	ChemComp-SO4 / SULFATE ION / Sulfate Mass: 96.063 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: SO₄
#3: Chemical	ChemComp-COA / COENZYME A / Coenzyme A Mass: 767.534 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂₁H₃₆N₇O₁₆P₃S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical	ChemComp-NH4 / AMMONIUM ION / Ammonium Mass: 18.038 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: H₄N / Feature type: SUBJECT OF INVESTIGATION
#5: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 1020 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.99 Å³/Da / Density % sol: 58.83 % / Mosaicity: 0.2 °
Crystal grow	Temperature: 289 K / Method: vapor diffusion / pH: 5.5 Details: 0.2 M (NH4)2SO4, 1 M Li2SO4, 0.1 M sodium citrate pH 5.5, 1 mM DTT, 1 mM EDTA, 1 mM NaN3

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

Australian Synchrotron

/ Beamline: MX1 / Wavelength: 0.9537 Å

Detector

Type: ADSC QUANTUM 210r / Detector: CCD / Date: Jul 5, 2018

Radiation

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

Radiation wavelength

Wavelength: 0.9537 Å / Relative weight: 1

Reflection

Resolution: 2.295→46.62 Å / Num. obs: 87824 / % possible obs: 99.8 % / Redundancy: 7.6 % / CC_1/2: 0.933 / R_merge(I) obs: 0.601 / R_pim(I) all: 0.234 / R_rim(I) all: 0.645 / Net I/σ(I): 4.1

Reflection shell

Diffraction-ID: 1 / Redundancy: 6.8 %

Resolution (Å)	R_merge(I) obs	Num. unique obs	CC_1/2	R_pim(I) all	R_rim(I) all	% possible all
2.295-2.34	2.756	4358	0.304	1.127	2.984	96.9
12.36-46.62	0.106	608	0.996	0.043	0.115	98.3

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Phasing

Phasing

Method:

molecular replacement

Phasing MR

	Highest resolution	Lowest resolution
Rotation	7.85 Å	46.62 Å
Translation	7.85 Å	46.62 Å

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Processing

Software

Name	Version	Classification
PHENIX	1.15_3459	refinement
XDS		data reduction
Aimless	0.7.2	data scaling
PHASER	2.8.3	phasing
PDB_EXTRACT	3.27	data extraction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1qfl

1qfl

Resolution: 2.295→44.62 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 27.25 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2648	4323	4.93 %
R_work	0.2288	83356	-
obs	0.2305	87679	99.69 %

Solvent computation

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

Displacement parameters

B_iso max: 122.63 Å² / B_iso mean: 41.0842 Å² / B_iso min: 5.2 Å²

Refinement step

Cycle: final / Resolution: 2.295→44.62 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	11176	0	251	1020	12447
B_iso mean	-	-	57.16	35.81	-
Num. residues	-	-	-	-	1560

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / R_factor R_free error: 0

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	% reflection obs (%)
2.2952-2.3213	0.358	145	0.3305	2611	94
2.3213-2.3486	0.3675	149	0.3145	2743	100
2.3486-2.3772	0.3491	136	0.3034	2742	100
2.3772-2.4073	0.3406	130	0.2936	2826	100
2.4073-2.439	0.29	122	0.2973	2729	100
2.439-2.4724	0.3197	176	0.2912	2746	99
2.4724-2.5077	0.3474	155	0.2908	2717	100
2.5077-2.5451	0.354	161	0.2799	2799	100
2.5451-2.5849	0.3337	147	0.3007	2736	100
2.5849-2.6273	0.3367	153	0.2911	2805	100
2.6273-2.6726	0.3442	111	0.2844	2752	100
2.6726-2.7212	0.3553	139	0.2925	2834	100
2.7212-2.7735	0.276	127	0.2761	2720	100
2.7735-2.8301	0.3575	142	0.263	2826	100
2.8301-2.8916	0.2912	128	0.2631	2798	100
2.8916-2.9589	0.302	169	0.2607	2719	100
2.9589-3.0329	0.2921	166	0.2505	2785	100
3.0329-3.1149	0.2723	165	0.2459	2753	100
3.1149-3.2065	0.2767	148	0.2211	2764	100
3.2065-3.31	0.2624	147	0.2141	2794	100
3.31-3.4282	0.2524	157	0.2086	2764	100
3.4282-3.5654	0.232	157	0.193	2761	100
3.5654-3.7276	0.2345	127	0.1899	2827	100
3.7276-3.924	0.2339	145	0.1867	2773	100
3.924-4.1697	0.1816	147	0.1711	2811	100
4.1697-4.4914	0.1725	131	0.1617	2797	100
4.4914-4.9428	0.1749	124	0.1656	2859	100
4.9428-5.6569	0.2308	138	0.1971	2806	100
5.6569-7.1224	0.2401	147	0.22	2835	100
7.1224-44.62	0.2298	134	0.2218	2924	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	0.6997	0.4873	-0.9233	0.5629	0.4155	2.0131	-0.1368	-0.0385	0.0403	0.0691	-0.1069	0.0717	-0.0726	0.0078	0.211	0.1333	0.034	-0.0044	0.1186	0.0036	0.2916	36.9861	-6.8822	8.7411
2	1.9175	-0.5536	-0.4528	0.41	0.3302	0.9213	0.0333	-0.0391	0.0468	-0.0372	0.0323	-0.1456	-0.015	0.088	-0.0557	0.1241	0.0104	0.0227	0.1145	-0.0156	0.2761	31.5161	2.0262	4.4022
3	1.5835	-0.1112	-0.7032	1.6447	-0.9492	4.2408	-0.1425	-0.216	0.0133	0.2654	0.1768	0.0258	0.1982	-0.1176	-0.0985	0.0956	-0.0134	-0.0288	0.0927	-0.0372	0.1968	21.7199	-1.0441	19.6824
4	2.0304	-0.6623	-1.1252	2.0079	0.3105	1.1464	-0.0731	-0.2756	-0.6284	0.0683	-0.0092	0.2056	0.1025	-0.0387	0.0865	0.1654	0.0236	-0.0089	0.1898	0.0527	0.3547	24.6056	-24.0337	13.9128
5	7.0691	-1.8513	-2.5822	9.4238	3.5466	5.8303	-0.1566	-0.382	0.4264	0.2398	0.8088	-0.6052	-0.3616	1.0124	-0.5999	0.0862	-0.0135	-0.0288	0.2197	0.0654	0.4089	46.9434	-7.9084	12.3101
6	2.6461	0.6942	-0.9464	5.1726	-1.9042	2.1014	-0.0662	-0.753	-0.5458	0.3341	-0.0202	-0.2192	0.2465	0.4222	0.1271	0.3644	0.0992	-0.0673	0.3072	0.0646	0.3221	37.1942	-26.0553	19.6694
7	1.3639	-0.3803	0.3261	1.5235	-0.3317	1.9929	0.0341	-0.0347	0.0937	-0.0558	-0.0044	0.1121	0.1309	0.0824	-0.0583	0.0718	0.0145	0.0448	0.1131	-0.0468	0.4006	30.5685	-11.7387	1.1925
8	1.7584	-0.0227	-2.5944	0.8704	-0.9297	4.9188	-0.0703	0.2586	-0.1948	-0.0252	-0.0322	0.2154	0.2117	-0.3935	0.113	0.1949	-0.0529	-0.0705	0.139	-0.0134	0.2954	23.7681	-20.8144	-2.9304
9	2.7376	0.6352	1.0265	2.0279	0.9414	5.0363	0.0625	-0.0399	-0.5933	0.1184	0.0484	0.0637	0.2147	-0.167	-0.1158	0.1495	0.024	0.0442	0.1233	0.0444	0.3608	30.0022	-25.1568	3.8616
10	2.3009	-0.7066	-1.5321	2.3659	0.7459	4.5699	-0.1707	0.042	-0.1666	-0.0478	-0.0612	-0.1094	0.155	0.2095	0.2423	0.1261	0.0003	0.0097	0.0895	0.0082	0.2559	32.6933	-15.011	-1.8706
11	1.314	0.0143	1.5867	2.9731	0.7774	8.1241	-0.115	-0.1929	-0.0946	0.0813	0.0965	0.1576	-0.0332	-0.1226	0.0009	0.1074	0.0329	0.0153	0.0759	0.0521	0.1953	5.088	6.9991	8.7769
12	1.0146	-0.3462	0.1402	0.899	0.0101	0.998	-0.0757	-0.0743	0.0638	0.1598	0.1029	0.0569	-0.0536	0.0483	-0.0192	0.1213	0.0187	0.0238	0.139	0.0222	0.2747	14.8946	7.2181	10.837
13	6.2008	-0.6573	-0.165	6.5282	-0.3569	2.9653	-0.0653	-0.1399	-0.4214	0.3157	0.2612	0.5691	0.194	-0.2623	-0.1539	0.04	0.0026	0.002	0.2781	-0.0038	0.361	-4.7575	8.1257	12.313
14	1.349	-0.2404	0.3716	1.5029	0.4835	2.4123	-0.0092	-0.0734	0.2487	0.0355	0.0046	-0.1355	-0.2257	0.0489	0	0.1098	0.006	0.0117	0.1297	0.0103	0.3538	12.9933	18.7579	3.5348
15	1.9828	-0.4344	-0.0212	2.3299	-0.0179	2.6365	-0.08	0.0602	-0.0696	-0.0624	-0.0244	0.1018	-0.0138	-0.1276	0.0944	0.1051	-0.0154	-0.0019	0.0943	-0.0159	0.236	9.0056	17.6367	-0.2981
16	1.1623	0.0971	0.3838	0.8178	0.2639	2.0542	0.2628	0.0086	-0.1866	0.4886	-0.209	0.2845	0.3183	-0.0075	-0.0559	1.1055	0.0733	-0.2023	0.3254	0.0138	0.2017	29.5981	-12.5554	60.8913
17	0.7035	0.2086	0.0624	0.3578	0.3379	1.6056	0.0393	-0.092	-0.0502	0.3222	-0.0313	-0.1322	-0.1026	0.1072	-0.0118	0.6218	0.0709	-0.0949	0.2788	-0	0.2979	32.3403	0.7527	55.8674
18	3.5723	1.9233	-1.6005	4.9836	-1.9649	1.7947	0.2119	0.4029	-0.2916	0.2392	-0.0245	-0.4512	0.4325	0.3757	-0.174	0.7433	0.1748	-0.1501	0.4341	0.0128	0.4133	46.0567	-11.73	51.7087
19	2.1826	0.6781	-1.1834	3.0146	-0.5533	2.121	-0.058	-0.1971	0.214	0.2123	-0.1571	0.1027	-0.0665	0.2671	0.1969	0.5719	0.0082	-0.1821	0.3105	-0.037	0.3018	37.137	-3.2039	66.6235
20	3.1312	0.1191	-0.8881	1.4884	-1.9298	5.7257	0.1813	-0.0856	0.1849	-0.3655	-0.2378	0.3659	-0.4592	0.2648	0.0632	0.7448	0.0129	-0.1024	0.2841	-0.0488	0.3785	42.5226	6.7189	70.5542
21	2.9938	0.9738	0.0525	3.3934	1.3794	2.4203	-0.1426	-0.0637	0.5743	-0.102	-0.0655	0.2424	-0.1854	-0.1178	0.212	0.612	0.0372	-0.109	0.3688	-0.0171	0.3652	48.8638	3.013	63.6082
22	6.2863	-1.0413	0.9566	3.3187	-0.2261	5.2375	-0.3766	-0.4847	-0.171	0.7574	-0.0454	-0.304	0.0315	0.3454	0.3933	0.6543	0.0298	-0.1512	0.3092	0.0325	0.3195	41.4524	-3.7862	69.6031
23	3.0551	-0.1115	0.5306	0.8435	1.1015	2.8219	0.0879	-0.1006	0.4251	0.35	-0.2981	0.1125	-0.3417	-0.2288	0.1875	0.7505	0.0424	0.0544	0.2303	-0.0053	0.3813	14.5674	12.8667	61.4348
24	0.2544	0.2781	0.2469	0.3117	0.8577	3.4011	0.0248	-0.1251	0.0009	0.3774	-0.0367	-0.0294	0.0896	-0.0581	0.0133	0.663	0.0575	-0.022	0.3184	0.0178	0.2366	20.5032	3.8734	57.4216
25	2.022	6.1189	-1.9996	7.5095	-3.2916	3.3371	-0.0056	-0.567	-0.7855	0.4439	-0.5089	1.0737	0.7493	-0.316	0.4485	0.9727	-0.0847	0.2553	0.4544	-0.092	0.9005	5.0565	-12.5936	53.3868
26	8.4728	5.8659	-0.4515	2.0541	0.4364	2.6446	0.0059	0.4998	0.2766	0.2628	0.0541	0.9081	-0.3539	-0.853	0.0999	0.5875	0.1761	0.1498	0.5844	-0.0649	0.7654	-3.6736	10.6461	57.3876
27	2.9639	0.2103	0.2163	0.2576	0.3027	0.3647	0.194	0.0621	0.3069	0.2799	-0.8298	1.9871	0.069	-1.06	0.611	0.5932	0.0877	0.2459	1.0745	-0.0857	1.2137	-8.1935	3.5255	50.4715
28	2.977	1.699	1.6518	1.6148	1.139	4.3846	0.2198	-0.4299	-0.546	0.1452	-0.2976	-0.1396	0.4691	-0.7815	0.0839	0.5431	-0.0008	0.1599	0.4095	0.012	0.521	7.0832	-0.6336	68.4827
29	4.8726	2.3328	-0.2937	2.1924	-1.4087	2.7443	-0.1104	-0.1927	-0.237	0.2055	-0.1717	0.4646	0.5518	-0.4754	0.2875	0.5315	-0.0184	0.1357	0.4562	-0.0414	0.5226	-1.5699	0.8599	68.4133
30	5.4697	-1.8864	-1.8978	4.7498	-0.859	8.6115	0.5565	-0.5311	0.3045	-0.5856	0.5029	-0.4477	-0.1837	-0.3164	-1.0621	0.641	-0.125	0.1029	0.4232	-0.0378	0.4225	5.0243	-0.3548	72.9492

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 3 through 26 )	A	3 - 26
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 27 through 104 )	A	27 - 104
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 105 through 141 )	A	105 - 141
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 142 through 191 )	A	142 - 191
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 192 through 213 )	A	192 - 213
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 214 through 234 )	A	214 - 234
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 235 through 284 )	A	235 - 284
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 285 through 319 )	A	285 - 319
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 320 through 349 )	A	320 - 349
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 350 through 392 )	A	350 - 392
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 3 through 26 )	B	3 - 26
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 27 through 191 )	B	27 - 191
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 192 through 213 )	B	192 - 213
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 214 through 330 )	B	214 - 330
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 331 through 392 )	B	331 - 392
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 3 through 65 )	C	3 - 65
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 66 through 191 )	C	66 - 191
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 192 through 234 )	C	192 - 234
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 235 through 284 )	C	235 - 284
20	X-RAY DIFFRACTION	20	chain 'C' and (resid 285 through 319 )	C	285 - 319
21	X-RAY DIFFRACTION	21	chain 'C' and (resid 320 through 349 )	C	320 - 349
22	X-RAY DIFFRACTION	22	chain 'C' and (resid 350 through 392 )	C	350 - 392
23	X-RAY DIFFRACTION	23	chain 'D' and (resid 3 through 65 )	D	3 - 65
24	X-RAY DIFFRACTION	24	chain 'D' and (resid 66 through 141 )	D	66 - 141
25	X-RAY DIFFRACTION	25	chain 'D' and (resid 142 through 171 )	D	142 - 171
26	X-RAY DIFFRACTION	26	chain 'D' and (resid 172 through 213 )	D	172 - 213
27	X-RAY DIFFRACTION	27	chain 'D' and (resid 214 through 234 )	D	214 - 234
28	X-RAY DIFFRACTION	28	chain 'D' and (resid 235 through 303 )	D	235 - 303
29	X-RAY DIFFRACTION	29	chain 'D' and (resid 304 through 368 )	D	304 - 368
30	X-RAY DIFFRACTION	30	chain 'D' and (resid 369 through 392 )	D	369 - 392

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