PDB-4e1l: Crystal structure of Acetoacetyl-CoA thiolase (thlA2) from Clostr...

ID or keywords:

Entry

Database: PDB / ID: 4e1l

Title

Crystal structure of Acetoacetyl-CoA thiolase (thlA2) from Clostridium difficile

Components

Acetoacetyl-CoA thiolase 2

Keywords

TRANSFERASE / 3-layer(aba) sandwich / thiolase / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID

Function / homology

Function and homology information

acetyl-CoA C-acetyltransferase / acetyl-CoA C-acetyltransferase activity
Similarity search - Function

Biological species

Clostridium difficile (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2 Å

Authors

Anderson, S.M. / Wawrzak, Z. / Kudritska, M. / Peterson, S.N. / Anderson, W.F. / Savchenko, A. / Center for Structural Genomics of Infectious Diseases (CSGID)

Citation

Journal: Microbiol Resour Announc / Year: 2023
Title: A high-throughput structural system biology approach to increase structure representation of proteins from Clostridioides difficile.
Authors: Rosas-Lemus, M. / Dey, S. / Minasov, G. / Tan, K. / Anderson, S.M. / Brunzelle, J. / Nocadello, S. / Shabalin, I. / Filippova, E. / Halavaty, A. / Kim, Y. / Maltseva, N. / Osipiuk, J. / ...

History

Deposition	Mar 6, 2012	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Mar 21, 2012	Provider: repository / Type: Initial release
Revision 1.1	Sep 13, 2023	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 / struct_ref_seq_dif / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2	Apr 29, 2026	Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4e1l.cif.gz	571.6 KB	Display	PDBx/mmCIF format
PDB format	pdb4e1l.ent.gz	474.1 KB	Display	PDB format
PDBx/mmJSON format	4e1l.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/e1/4e1l ftp://data.pdbj.org/pub/pdb/validation_reports/e1/4e1l	HTTPS FTP

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Related structure data

Related structure data	3sd7C 3srtC 3uuwC 4dd5C 4dgtC 4dq6C 4dunC 4eguC 4gibC 4h3dC 4isxC 4jjpC 4kd5C 4mfgC 4nmyC 4rn7C 5dzsC 5ttaC 5tv7C 5txuC 6n7mC 6ue2C 6wy4C 7k1uC 7rl8C 7rlrC 1m3zS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	7k5j-5 7k5j-3 7k5j-2 7k5j-1 5akh-1 7k5j-8 7k5j-7 6s3z-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
Other databases	TargetTrack: IDP05528

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#216 - Dec 2017 Biodegradable Plastic similarity (13) #90 - Jun 2007 Fatty Acid Synthase similarity (1)

Deposited unit

A: Acetoacetyl-CoA thiolase 2

B: Acetoacetyl-CoA thiolase 2

C: Acetoacetyl-CoA thiolase 2

D: Acetoacetyl-CoA thiolase 2

hetero molecules

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

1

Idetical with deposited unit
defined by author

Unit cell

Length a, b, c (Å)	103.32, 78.92, 127.03
Angle α, β, γ (deg.)	90.0, 112.73, 90.0
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Acetoacetyl-CoA thiolase 2 Mass: 41690.883 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Clostridium difficile (bacteria) / Strain: 630 / Gene: thlA2, CD630_26760 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIPL / References: UniProt: Q183B0, acetyl-CoA C-acetyltransferase
#2: Chemical	... ChemComp-IOD / IODIDE ION Mass: 126.904 Da / Num. of mol.: 57 / Source method: obtained synthetically / Formula: I
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 871 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	N

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.86 Å³/Da / Density % sol: 57.06 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 20% PEG3350, 200mM Sodium Iodide, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction

Mean temperature: 110 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 21-ID-D / Wavelength: 1.12714 Å

Detector

Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 9, 2011 / Details: bimorph KB mirrors

Radiation

Monochromator: Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 1.12714 Å / Relative weight: 1

Reflection

Resolution: 2→39.2 Å / Num. all: 126930 / Num. obs: 125788 / % possible obs: 99.1 % / Observed criterion σ(F): 1.5 / Observed criterion σ(I): 2.2 / Redundancy: 4.9 % / B_iso Wilson estimate: 30.57 Å² / R_merge(I) obs: 0.076 / Χ²: 1.003 / Net I/σ(I): 16.29

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. unique all	Χ²	% possible all
2-2.07	3.9	0.622	2.16	12004	0.992	95
2.07-2.15	4.3	0.48	3.06	12347	0.999	98
2.15-2.25	4.6	0.367	4.22	12531	1.006	99.1
2.25-2.37	4.7	0.272	5.74	12550	0.997	99.5
2.37-2.52	4.8	0.198	7.93	12643	1.011	99.8
2.52-2.71	5	0.142	10.75	12660	1.011	99.9
2.71-2.99	5.2	0.094	15.09	12657	1.002	100
2.99-3.42	5.3	0.069	18.86	12733	1.012	100
3.42-4.31	5.4	0.052	21.98	12735	1.008	100
4.31-39.17	5.2	0.042	25.25	12928	0.992	99.7

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Processing

Software

Name	Version	Classification
SCALEPACK		data scaling
PHENIX	1.7.2_869	refinement
PDB_EXTRACT	3.1	data extraction
BLU-MAX		data collection
HKL-2000		data reduction
HKL-2000		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB entry 1M3Z

1m3z

Resolution: 2→39.05 Å / Occupancy max: 1 / Occupancy min: 0.33 / FOM work R set: 0.855 / SU ML: 0.53 / σ(F): 1.34 / Phase error: 21.75 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2072	6283	5 %	random
R_work	0.1749	-	-	-
all	0.1766	127302	-	-
obs	0.1765	125737	98.77 %	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 48.092 Å² / k_sol: 0.345 e/Å³

Displacement parameters

B_iso max: 171.23 Å² / B_iso mean: 40.9055 Å² / B_iso min: 16.86 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	9.461 Å²	-0 Å²	3.4247 Å²
2-	-	0.5974 Å²	0 Å²
3-	-	-	-10.0583 Å²

Refinement step

Cycle: LAST / Resolution: 2→39.05 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	11031	0	57	871	11959

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	11169
X-RAY DIFFRACTION	f_angle_d	1.094	15077
X-RAY DIFFRACTION	f_chiral_restr	0.073	1802
X-RAY DIFFRACTION	f_plane_restr	0.005	1968
X-RAY DIFFRACTION	f_dihedral_angle_d	12.621	4191

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	Num. reflection obs	% reflection obs (%)
2-2.07	0.2692	590	0.2347	3389	3576	11649	91.9
2.07-2.16	0.2509	623	0.2219	3811	4005	12366	98
2.16-2.25	0.2321	626	0.1934	3849	4058	12585	99.1
2.25-2.37	0.2355	629	0.1838	3901	4112	12596	99.5
2.37-2.52	0.2364	629	0.1767	3916	4108	12691	99.8
2.52-2.71	0.1885	640	0.173	3920	4140	12676	99.9
2.71-2.99	0.2126	627	0.1769	4015	4227	12689	100
2.99-3.42	0.1937	639	0.1657	3941	4134	12763	100
3.42-4.31	0.1636	633	0.1422	4000	4221	12786	100
4.31-39.18	0.2122	647	0.1927	3960	4173	12970	99.8

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	0.6015	-0.0091	-0.029	0.6846	-0.3741	0.3353	-0.0743	-0.0797	0.1904	-0.158	0.0558	0.096	-0.1793	-0.199	0.0038	0.1806	0.036	-0.0017	0.2446	-0.0257	0.2612	23.1002	64.0559	112.4978
2	0.4638	-0.2809	0.07	0.2294	0.0376	0.4555	-0.0044	0.0248	0.0572	-0.0044	0.0424	-0.1057	-0.0243	0.0188	-0	0.1942	0.0228	-0.0138	0.2328	-0.0008	0.2573	30.3516	62.0032	111.257
3	0.218	0.0096	0.176	0.1248	0.0261	0.1419	-0.0644	0.1015	-0.2595	-0.2299	-0.1858	-0.2402	0.2199	0.2181	-0.0001	0.325	0.0171	0.0062	0.2669	0.0174	0.343	29.7675	37.6176	103.8473
4	0.8062	0.0032	0.0069	1.0709	0.0202	1.2589	-0.0113	-0.344	-0.1075	0.1133	0.0125	0.0647	0.1007	-0.1939	-0.0019	0.1495	0.0001	0.0089	0.3166	0.0461	0.234	24.6519	48.4005	122.9792
5	0.0943	0.0824	-0.1706	0.1935	-0.174	0.297	-0.0107	0.0309	0.0099	0.0071	-0.0266	-0.103	0.0503	0.0611	-0.0024	0.3114	-0.0102	-0.01	0.1401	-0.0126	0.1869	25.3615	47.5735	67.9989
6	0.3182	-0.0985	-0.0171	0.3637	0.1873	0.1312	0.0681	-0.0301	0.1274	-0.0682	-0.0183	-0.0255	-0.3306	-0.1007	0.0152	0.3414	0.0082	0.0238	0.1424	-0.0004	0.2136	20.5832	56.5842	70.0642
7	0.1064	-0.0199	0.0021	0.2811	0.2593	0.267	0.0898	-0.0875	0.0057	-0.0181	-0.0612	0.0544	0.0312	-0.2407	0.0002	0.3033	-0.0269	0.0041	0.1877	-0.0105	0.2172	15.4473	51.1032	71.4632
8	0.1195	0.094	0.1129	0.071	0.0856	0.0982	0.0934	-0.2315	-0.0085	0.0328	-0.2015	0.1956	0.3687	-0.285	-0.0024	0.4187	-0.0902	0.011	0.2579	-0.0139	0.2497	19.6858	33.4477	88.7031
9	0.8818	-0.5538	0.4031	1.3246	-0.1533	1.0485	0.058	0.0472	0.008	0.0783	-0.0288	-0.1554	0.1419	0.1719	-0.0219	0.3681	0.0064	0.0023	0.1524	-0.0236	0.1778	31.2932	36.4612	70.8667
10	0.415	-0.2246	0.0516	0.6671	0.3716	0.2892	0.0712	-0.0524	-0.0954	-0.0349	-0.1329	0.2194	0.1386	-0.2173	-0.0076	0.3986	-0.1051	-0.045	0.2182	-0.0279	0.2614	10.054	35.2263	64.8859
11	0.5491	0.0509	-0.2726	0.6678	-0.116	0.2411	0.0435	0.0636	-0.0875	-0.1361	-0.0291	0.0795	0.3317	-0.1017	0.035	0.4382	-0.044	-0.0232	0.1613	-0.0289	0.2162	20.1287	32.77	64.128
12	0.231	-0.0122	-0.271	0.6809	-0.4702	0.9751	-0.1973	-0.1415	0.0028	-0.1514	-0.0793	-0.1516	0.3801	0.0309	-0.1596	0.2334	-0.0231	0.0329	0.222	-0.0279	0.2354	53.4208	58.0762	98.1796
13	1.1334	0.2679	-0.7535	1.249	-0.2215	0.8067	-0.1703	-0.0573	-0.1671	-0.1948	0.0735	0.0654	0.0278	-0.0328	-0.0187	0.1707	0.0066	0.0053	0.1764	0.0093	0.2714	47.1154	54.1488	104.5608
14	0.1655	0.0335	0.2048	0.2756	0.0413	0.4801	-0.1809	0.3267	0.3143	-0.3398	0.0673	-0.0554	-0.2393	0.1027	-0	0.4873	-0.088	-0.0422	0.3153	0.0497	0.3012	45.5388	76.3303	83.9538
15	0.3148	-0.1727	0.2297	0.0925	-0.125	0.1648	-0.1371	0.178	-0.2518	-0.3121	0.0032	-0.4288	0.4164	0.5374	-0.0859	0.3945	-0.0011	0.1345	0.3822	-0.074	0.4613	62.4337	55.4854	90.4312
16	0.1853	0.1163	0.0174	0.5569	-0.177	0.1829	0.0384	0.4716	-0.0963	-0.6069	-0.0055	-0.0965	0.2906	0.1554	0.0082	0.5329	-0.1201	-0.0191	0.4038	0.0283	0.2424	46.2406	68.9442	78.5731
17	0.2974	0.2379	-0.3313	0.602	-0.2561	0.3669	-0.0561	-0.1851	-0.0678	0.0756	-0.0378	-0.1666	-0.0401	0.2173	-0.0001	0.1474	-0.0135	-0.0414	0.3039	0.0074	0.2667	56.065	63.9436	112.0729
18	0.8389	0.339	-0.226	0.6628	-0.2858	0.922	-0.0852	-0.007	0.2257	-0.1562	0.0718	0.0155	-0.1832	0.1012	-0.0018	0.2747	-0.0586	-0.0391	0.1984	-0.0037	0.2707	49.0727	74.9975	98.8969
19	0.987	-0.3301	-0.4909	0.8319	0.0455	0.587	-0.0522	-0.2109	-0.081	-0.1177	-0.0519	0.0234	0.1787	-0.4	-0.007	0.2729	-0.0875	0.0127	0.4971	-0.043	0.357	-2.1359	45.1768	81.9614
20	0.0694	0.152	-0.0141	0.332	-0.0195	0.0098	0.0613	-0.1491	-0.0375	-0.1298	-0.0855	-0.0193	-0.2816	-0.2216	-0.1818	0.2922	0.1124	0.0661	0.5765	-0.1719	0.4818	-2.4249	73.5509	89.0346
21	1.1612	0.1273	0.039	0.556	-0.091	0.1522	0.078	-0.1366	-0.1431	0.1487	0.0387	0.177	-0.0542	-0.2591	1.3814	0.1775	-0.0092	0.1269	0.7841	-0.0663	0.3839	-14.6011	52.2461	96.581
22	0.7825	-0.6496	-0.5841	0.8541	0.2094	0.8534	0.0711	-0.0486	0.1588	-0.2983	-0.1172	0.1002	-0.2843	-0.4992	-0.0164	0.2163	0.0708	-0.0233	0.4809	-0.09	0.2741	-5.5278	63.1823	78.6623

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 (RESSEQ 1:72)	A	1 - 72
2	X-RAY DIFFRACTION	2	CHAIN A AND (RESSEQ 73:124)	A	73 - 124
3	X-RAY DIFFRACTION	3	CHAIN A AND (RESSEQ 125:168)	A	125 - 168
4	X-RAY DIFFRACTION	4	CHAIN A AND (RESSEQ 169:392)	A	169 - 392
5	X-RAY DIFFRACTION	5	CHAIN B AND (RESSEQ 1:25)	B	1 - 25
6	X-RAY DIFFRACTION	6	CHAIN B AND (RESSEQ 26:72)	B	26 - 72
7	X-RAY DIFFRACTION	7	CHAIN B AND (RESSEQ 73:124)	B	73 - 124
8	X-RAY DIFFRACTION	8	CHAIN B AND (RESSEQ 125:168)	B	125 - 168
9	X-RAY DIFFRACTION	9	CHAIN B AND (RESSEQ 169:267)	B	169 - 267
10	X-RAY DIFFRACTION	10	CHAIN B AND (RESSEQ 268:304)	B	268 - 304
11	X-RAY DIFFRACTION	11	CHAIN B AND (RESSEQ 305:392)	B	305 - 392
12	X-RAY DIFFRACTION	12	CHAIN C AND (RESSEQ 1:25)	C	1 - 25
13	X-RAY DIFFRACTION	13	CHAIN C AND (RESSEQ 26:155)	C	26 - 155
14	X-RAY DIFFRACTION	14	CHAIN C AND (RESSEQ 156:191)	C	156 - 191
15	X-RAY DIFFRACTION	15	CHAIN C AND (RESSEQ 192:214)	C	192 - 214
16	X-RAY DIFFRACTION	16	CHAIN C AND (RESSEQ 215:251)	C	215 - 251
17	X-RAY DIFFRACTION	17	CHAIN C AND (RESSEQ 252:283)	C	252 - 283
18	X-RAY DIFFRACTION	18	CHAIN C AND (RESSEQ 284:392)	C	284 - 392
19	X-RAY DIFFRACTION	19	CHAIN D AND (RESSEQ 1:154)	D	1 - 154
20	X-RAY DIFFRACTION	20	CHAIN D AND (RESSEQ 155:191)	D	155 - 191
21	X-RAY DIFFRACTION	21	CHAIN D AND (RESSEQ 192:225)	D	192 - 225
22	X-RAY DIFFRACTION	22	CHAIN D AND (RESSEQ 226:392)	D	226 - 392

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