PDB-5dbn: Crystal structure of AtoDA complex

ID or keywords:

Entry

Database: PDB / ID: 5dbn

Title

Crystal structure of AtoDA complex

Components

(Acetate CoA-transferase subunit ...

) x 2

Keywords

TRANSFERASE /

protein complex / acetoacetyl-CoA transferase /

protein binding

Function / homology

Function and homology information

butyrate-acetoacetate CoA-transferase activity /

acetate CoA-transferase /

CoA-transferase activity / short-chain fatty acid metabolic process /

acetate CoA-transferase activity /

cytoplasm
Similarity search - Function

Biological species

Escherichia coli DH5[alpha] (bacteria)

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 2.549 Å

Authors

Arbing, M.A. / Koo, C.W. / Shin, A. / Medrano-Soto, A. / Eisenberg, D.

Citation

Journal: To Be Published
Title: Crystal structure of AtoDA complex
Authors: Arbing, M.A. / Koo, C.W. / Shin, A. / Medrano-Soto, A. / Eisenberg, D.

History

Deposition	Aug 21, 2015	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Aug 24, 2016	Provider: repository / Type: Initial release
Revision 1.1	Nov 27, 2019	Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list / Item: _pdbx_struct_oper_list.symmetry_operation
Revision 1.2	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	5dbn.cif.gz	914.7 KB	Display	PDBx/mmCIF format
PDB format	pdb5dbn.ent.gz	778.7 KB	Display	PDB format
PDBx/mmJSON format	5dbn.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/db/5dbn ftp://data.pdbj.org/pub/pdb/validation_reports/db/5dbn	HTTPS FTP

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Related structure data

Related structure data	1k6dS S: Starting model for refinement
Similar structure data	2kau-d 1fwg-d 1krc-d 4ep8-d 1a5o-d 3wzf-1 1fwd-d 1fwj-d 1fwh-d 4epb-d 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

Deposited unit

A: Acetate CoA-transferase subunit alpha

B: Acetate CoA-transferase subunit beta

C: Acetate CoA-transferase subunit alpha

D: Acetate CoA-transferase subunit beta

E: Acetate CoA-transferase subunit alpha

F: Acetate CoA-transferase subunit beta

G: Acetate CoA-transferase subunit alpha

H: Acetate CoA-transferase subunit beta

hetero molecules

191 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Acetate CoA-transferase subunit alpha

B: Acetate CoA-transferase subunit beta

C: Acetate CoA-transferase subunit alpha

D: Acetate CoA-transferase subunit beta

hetero molecules

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

2

E: Acetate CoA-transferase subunit alpha

F: Acetate CoA-transferase subunit beta

G: Acetate CoA-transferase subunit alpha

H: Acetate CoA-transferase subunit beta

hetero molecules

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

Unit cell

Length a, b, c (Å)	73.680, 175.680, 76.160
Angle α, β, γ (deg.)	90.00, 113.01, 90.00
Int Tables number	4
Space group name H-M	P12₁1

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Acetate CoA-transferase subunit ... , 2 types, 8 molecules ACEGBDFH

#1: Protein	Acetate CoA-transferase subunit alpha / / Acetyl-CoA:acetoacetate-CoA transferase subunit alpha Mass: 23636.248 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli DH5[alpha] (bacteria) / Strain: DH5[alpha] / Gene: atoD, b2221, JW2215 / Plasmid: pMAPLe3 / Details (production host): pET28 derivative / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P76458, acetate CoA-transferase
#2: Protein	Acetate CoA-transferase subunit beta / / Acetyl-CoA:acetoacetate CoA-transferase subunit beta Mass: 23914.641 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli DH5[alpha] (bacteria) / Strain: DH5[alpha] / Gene: atoA, b2222, JW2216 / Plasmid: pMAPLe3 / Details (production host): pET28 derivative / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P76459, acetate CoA-transferase

#1: Protein

Acetate CoA-transferase subunit alpha /

/ Acetyl-CoA:acetoacetate-CoA transferase subunit alpha

Mass: 23636.248 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Escherichia coli DH5[alpha] (bacteria) / Strain: DH5[alpha] / Gene: atoD, b2221, JW2215 / Plasmid: pMAPLe3 / Details (production host): pET28 derivative / Production host:

Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P76458,

acetate CoA-transferase

#2: Protein

Acetate CoA-transferase subunit beta /

/ Acetyl-CoA:acetoacetate CoA-transferase subunit beta

Mass: 23914.641 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Escherichia coli DH5[alpha] (bacteria) / Strain: DH5[alpha] / Gene: atoA, b2222, JW2216 / Plasmid: pMAPLe3 / Details (production host): pET28 derivative / Production host:

Escherichia coli BL21 (bacteria) / References: UniProt: P76459,

acetate CoA-transferase

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Non-polymers , 5 types, 469 molecules

#3: Chemical	ChemComp-PO4 / PHOSPHATE ION / Phosphate Mass: 94.971 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: PO₄
#4: Chemical	ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol Mass: 106.120 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C₄H₁₀O₃
#5: Chemical	ChemComp-CL / CHLORIDE ION / Chloride Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₈O₃
#7: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 457 / 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: 2.48 Å³/Da / Density % sol: 50.45 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 1:1 protein to reservoir solution (0.2 M magnesium chloride, 0.1 M Bis-Tris, pH 6.5, 25% PEG3350), crystals grew in ~4 days, cryoprotectant: reservoir solution + 10% PEG400

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.54 Å

Detector

Type: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: Jul 10, 2014

Radiation

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

Radiation wavelength

Wavelength: 1.54 Å / Relative weight: 1

Reflection

Resolution: 2.55→87.84 Å / Num. obs: 57378 / % possible obs: 98.7 % / Observed criterion σ(I): -3 / Redundancy: 7.62 % / B_iso Wilson estimate: 30.42 Å² / R_merge F obs: 0.995 / R_merge(I) obs: 0.139 / R_rim(I) all: 0.149 / Χ²: 0.875 / Net I/σ(I): 14.71 / Num. measured all: 437267

Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)	Highest resolution (Å)	Redundancy (%)	R_merge F obs	R_merge(I) obs	Mean I/σ(I) obs	Num. measured obs	Num. possible	Num. unique obs	R_rim(I) all	% possible all
2.55-2.61		7.01	0.774	0.676	3.13	27545	4265	3928	0.729	92.1
2.61-2.69			0.856	0.549	4.12	31357	4171	4097	0.589	98.2
2.69-2.76			0.882	0.502	4.5	30720	4080	4018	0.538	98.5
2.76-2.85			0.913	0.426	5.32	30110	3969	3927	0.456	98.9
2.85-2.94			0.934	0.373	5.98	29153	3826	3798	0.399	99.3
2.94-3.05			0.952	0.313	6.99	28184	3705	3671	0.336	99.1
3.05-3.16			0.967	0.252	8.6	26838	3524	3497	0.27	99.2
3.16-3.29			0.977	0.211	10.32	26424	3473	3443	0.226	99.1
3.29-3.44			0.987	0.161	13.25	25063	3284	3269	0.173	99.5
3.44-3.6			0.991	0.131	15.86	24149	3173	3155	0.141	99.4
3.6-3.8			0.994	0.109	18.82	22770	2991	2980	0.117	99.6
3.8-4.03			0.995	0.093	21.4	21784	2854	2845	0.1	99.7
4.03-4.31			0.997	0.075	25.51	20413	2676	2664	0.081	99.6
4.31-4.65			0.998	0.059	30.36	19001	2492	2481	0.064	99.6
4.65-5.1			0.998	0.058	30.6	17601	2285	2282	0.062	99.9
5.1-5.7			0.997	0.071	25.48	16128	2086	2080	0.077	99.7
5.7-6.58			0.997	0.074	24.95	14136	1831	1821	0.079	99.5
6.58-8.06			0.999	0.054	32.44	12003	1559	1554	0.058	99.7
8.06-11.4			0.999	0.036	47.07	9234	1211	1207	0.038	99.7
	11.4		0.999	0.034	49.59	4654	681	661	0.036	97.1

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Phasing

Phasing	Method: molecular replacement

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Processing

Software

Name	Version	Classification
PHENIX	1.9_1692	refinement
XDS		data reduction
XSCALE		data scaling
PHASER		phasing
PDB_EXTRACT	3.15	data extraction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB entry 1K6D

1k6d

Resolution: 2.549→44.323 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.18 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2206	2868	5 %	Random selection
R_work	0.1877	-	-	-
obs	0.1894	57367	98.9 %	-

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.549→44.323 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	12606	0	67	457	13130

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.003	12849
X-RAY DIFFRACTION	f_angle_d	0.737	17435
X-RAY DIFFRACTION	f_dihedral_angle_d	10.515	4661
X-RAY DIFFRACTION	f_chiral_restr	0.029	2093
X-RAY DIFFRACTION	f_plane_restr	0.003	2268

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 (%)
2.5485-2.5924	0.3017	126	0.2623	2406	X-RAY DIFFRACTION	88
2.5924-2.6396	0.2762	145	0.2465	2757	X-RAY DIFFRACTION	99
2.6396-2.6903	0.3014	141	0.2402	2671	X-RAY DIFFRACTION	98
2.6903-2.7452	0.2955	144	0.241	2738	X-RAY DIFFRACTION	99
2.7452-2.8049	0.2773	143	0.2344	2720	X-RAY DIFFRACTION	99
2.8049-2.8702	0.2792	142	0.2266	2689	X-RAY DIFFRACTION	99
2.8702-2.9419	0.2795	145	0.2186	2768	X-RAY DIFFRACTION	99
2.9419-3.0215	0.2563	142	0.2222	2693	X-RAY DIFFRACTION	99
3.0215-3.1103	0.2718	144	0.2202	2725	X-RAY DIFFRACTION	99
3.1103-3.2107	0.2434	145	0.2205	2756	X-RAY DIFFRACTION	99
3.2107-3.3254	0.2544	144	0.2135	2737	X-RAY DIFFRACTION	99
3.3254-3.4585	0.2141	145	0.202	2758	X-RAY DIFFRACTION	100
3.4585-3.6159	0.215	143	0.1879	2726	X-RAY DIFFRACTION	100
3.6159-3.8064	0.2177	146	0.1778	2771	X-RAY DIFFRACTION	100
3.8064-4.0447	0.2144	144	0.1669	2739	X-RAY DIFFRACTION	100
4.0447-4.3568	0.1691	145	0.1516	2750	X-RAY DIFFRACTION	100
4.3568-4.7947	0.1513	145	0.1368	2757	X-RAY DIFFRACTION	100
4.7947-5.4875	0.1703	146	0.1469	2776	X-RAY DIFFRACTION	100
5.4875-6.9094	0.2255	146	0.1747	2775	X-RAY DIFFRACTION	100
6.9094-44.3294	0.1699	147	0.1563	2787	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	1.9919	-0.6725	0.4237	2.8249	-0.0995	1.9421	-0.2305	-0.4217	-0.2468	0.6954	0.2007	0.3781	0.0767	-0.1387	0.0399	0.4359	0.0979	0.1378	0.2537	0.0403	0.2486	7.1624	95.2249	27.7112
2	3.5216	-1.8823	0.6351	1.5151	-0.4916	2.0902	0.0855	0.1842	-0.2921	-0.1425	-0.0808	0.3454	0.0681	-0.2835	0.0035	0.2333	-0.0065	0.0057	0.1885	-0.0658	0.333	-6.6144	100.2306	1.6109
3	2.2969	0.4026	-0.0017	2.1909	-0.0719	1.6185	-0.0327	0.1749	0.1201	-0.0884	0.0198	-0.3354	-0.0188	0.204	0.011	0.1528	0.0337	0.0194	0.1822	0.0184	0.2219	27.3223	105.8173	4.9026
4	0.4752	0.5573	-0.0239	1.7337	1.3374	3.7031	0.1103	-0.3355	0.0765	0.2646	0.1605	-0.5354	0.0706	0.862	-0.2297	0.253	0.0553	-0.0671	0.5371	-0.1076	0.4245	38.5307	108.1386	32.5205
5	2.5048	0.4786	1.4089	1.9271	0.8911	3.9402	0.0321	0.58	-0.0451	-0.1195	0.0888	-0.4407	-0.1673	1.3321	-0.0868	0.1818	-0.03	0.08	0.6644	0.0262	0.2807	59.3307	58.4114	39.5902
6	0.9452	0.9313	1.0019	2.0798	1.6117	3.7034	-0.0812	0.2174	-0.0005	-0.1984	0.076	-0.1245	-0.2756	0.2034	0.0165	0.1977	0.0395	0.0512	0.2428	0.042	0.2141	40.1892	54.4414	17.0068
7	2.0374	-0.2542	0.2667	1.7737	-0.975	3.6676	0.0557	0.0201	0.1134	0.0453	0.0185	0.282	-0.3411	-0.4711	-0.0746	0.2114	0.0281	-0.0053	0.1723	0.0021	0.2085	28.9249	60.3634	49.2924
8	2.2708	-1.1859	1.3514	2.0318	-1.3931	3.1411	-0.1873	-0.4427	0.0323	0.3372	0.1737	-0.0398	-0.3177	-0.0511	0.0086	0.2178	0.0077	0.0412	0.2708	-0.0536	0.1805	48.0236	56.8327	72.0584

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain A
2	X-RAY DIFFRACTION	2	chain B
3	X-RAY DIFFRACTION	3	chain C
4	X-RAY DIFFRACTION	4	chain D
5	X-RAY DIFFRACTION	5	chain E
6	X-RAY DIFFRACTION	6	chain F
7	X-RAY DIFFRACTION	7	chain G
8	X-RAY DIFFRACTION	8	chain H

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