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)

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

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4e1l.cif.gz	571.5 KB	Display	PDBx/mmCIF format
PDB format	pdb4e1l.ent.gz	473.8 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	1m3zS S: Starting model for refinement
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

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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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