PDB-5dw5: Succinyl-CoA:acetate CoA-transferase (AarCH6) bound to the CoA an...

ID or keywords:

Entry

Database: PDB / ID: 5dw5

Title

Succinyl-CoA:acetate CoA-transferase (AarCH6) bound to the CoA analogue 3'-phosphoadenosine 5'-(O-(N-propylpantothenamide))pyrophosphate (MX)

Components

Succinyl-CoA:acetate CoA-transferase

Keywords

TRANSFERASE / Tricarboxylic acid cycle / Acidophile

Function / homology

Function and homology information

acetyl-CoA hydrolase activity / succinyl-CoA:acetate CoA-transferase / acetate catabolic process / propionate metabolic process, methylcitrate cycle / acetate CoA-transferase activity / acetate metabolic process / succinyl-CoA catabolic process / acetyl-CoA biosynthetic process from acetate / acetyl-CoA metabolic process / transferase activity
Similarity search - Function

Biological species

Acetobacter aceti (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

FOURIER SYNTHESIS / Resolution: 1.656 Å

Authors

Kappock, T.J. / Murphy, J.R.

Citation

Journal: Front Chem / Year: 2016
Title: Functional Dissection of the Bipartite Active Site of the Class I Coenzyme A (CoA)-Transferase Succinyl-CoA:Acetate CoA-Transferase.
Authors: Murphy, J.R. / Mullins, E.A. / Kappock, T.J.

History

Deposition	Sep 22, 2015	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	May 4, 2016	Provider: repository / Type: Initial release
Revision 1.1	Jun 8, 2016	Group: Database references
Revision 1.2	Sep 27, 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 / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list Item: _citation.country / _database_2.pdbx_DOI ..._citation.country / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	5dw5.cif.gz	418.1 KB	Display	PDBx/mmCIF format
PDB format	pdb5dw5.ent.gz	341.5 KB	Display	PDB format
PDBx/mmJSON format	5dw5.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	5dw5_validation.pdf.gz	919.6 KB	Display	wwPDB validaton report
Full document	5dw5_full_validation.pdf.gz	924.8 KB	Display
Data in XML	5dw5_validation.xml.gz	45.8 KB	Display
Data in CIF	5dw5_validation.cif.gz	68.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/dw/5dw5 ftp://data.pdbj.org/pub/pdb/validation_reports/dw/5dw5	HTTPS FTP

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Related structure data

Related structure data	5ddkC 5dw4C 5dw6C 5e5hC 4eu9S 4eu5 C: citing same article (ref.) S: Starting model for refinement
Similar structure data	5ddk-d 4eua-d 5dw6-d 2nvv-2 4eu5-d 2nvv-3 4eu3-d 4eub-d 4eu4-d 5dw4-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	#134 - Feb 2011 Integrin similarity (1) #172 - Apr 2014 RecA and Rad51 similarity (1) #194 - Feb 2016 Designer Insulins similarity (1) #234 - Jun 2019 MDM2 and Cancer similarity (1) #259 - Jul 2021 Designed Proteins and Citizen Science similarity (1)

Deposited unit

A: Succinyl-CoA:acetate CoA-transferase

B: Succinyl-CoA:acetate CoA-transferase

hetero molecules

114 kDa, 2 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)	67.477, 110.305, 120.144
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

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Protein , 1 types, 2 molecules AB

#1: Protein	Succinyl-CoA:acetate CoA-transferase Mass: 56046.289 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Acetobacter aceti (bacteria) / Strain: 1023 / Gene: AZ09_02565 / Plasmid: pET23a / Details (production host): pJK385 / Production host: Escherichia coli (E. coli) / Strain (production host): C41(DE3) References: UniProt: A0A063X8M7, UniProt: B3EY95*PLUS, succinyl-CoA:acetate CoA-transferase

#1: Protein

Succinyl-CoA:acetate CoA-transferase

Mass: 56046.289 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Acetobacter aceti (bacteria) / Strain: 1023 / Gene: AZ09_02565 / Plasmid: pET23a / Details (production host): pJK385 / Production host:

Escherichia coli (E. coli) / Strain (production host): C41(DE3)
References: UniProt: A0A063X8M7, UniProt: B3EY95*PLUS, succinyl-CoA:acetate CoA-transferase

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Non-polymers , 5 types, 895 molecules

#2: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#3: Chemical	ChemComp-0T1 / [[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-4-oxidanyl-3-phosphonooxy-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(3R)-2,2-dimethyl-3-oxidanyl-4-oxidanylidene-4-[[3-oxidanylidene-3-(propylamino)propyl]amino]butyl] hydrogen phosphate / DETHIACOENZYME A Mass: 749.496 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂₂H₃₈N₇O₁₆P₃
#4: Chemical	ChemComp-ACT / ACETATE ION Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂H₃O₂
#5: Chemical	ChemComp-IMD / IMIDAZOLE Mass: 69.085 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₃H₅N₂
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 885 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION

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Sample preparation

Crystal	Density Matthews: 1.99 Å³/Da / Density % sol: 38.33 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.2 Details: 0.9 M sodium citrate, 0.1 M imidazole, 25 mM 2-mercaptoethanol, 1 mM MX

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
Detector	Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 12, 2015
Radiation	Monochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97872 Å / Relative weight: 1
Reflection	Resolution: 1.656→50 Å / Num. obs: 106546 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.7 % / R_sym value: 0.059 / Net I/σ(I): 50.19
Reflection shell	Resolution: 1.656→1.69 Å / Redundancy: 7.1 % / R_merge(I) obs: 0.307 / Mean I/σ(I) obs: 6.1 / R_sym value: 0.307 / % possible all: 82.4

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Processing

Software

Name	Version	Classification
PHENIX	1.9_1692	refinement
HKL-2000		data reduction
SCALEPACK		data scaling
PHASER		phasing

Refinement

Method to determine structure:

FOURIER SYNTHESIS
Starting model: 4eu9

4eu9

Resolution: 1.656→44.868 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.49 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1737	5344	5.02 %	same as 4eu9
R_work	0.1504	-	-	-
obs	0.1516	106455	99.39 %	-

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.656→44.868 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7754	0	122	885	8761

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	8131
X-RAY DIFFRACTION	f_angle_d	1.124	11041
X-RAY DIFFRACTION	f_dihedral_angle_d	13.802	3035
X-RAY DIFFRACTION	f_chiral_restr	0.047	1217
X-RAY DIFFRACTION	f_plane_restr	0.006	1463

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 (%)
1.6564-1.6752	0.2076	157	0.1743	2885	X-RAY DIFFRACTION	86
1.6752-1.6949	0.1927	198	0.1704	3332	X-RAY DIFFRACTION	100
1.6949-1.7156	0.2213	160	0.1661	3360	X-RAY DIFFRACTION	100
1.7156-1.7373	0.2059	182	0.1643	3360	X-RAY DIFFRACTION	100
1.7373-1.7601	0.2064	186	0.1687	3323	X-RAY DIFFRACTION	100
1.7601-1.7842	0.2439	187	0.1651	3351	X-RAY DIFFRACTION	100
1.7842-1.8097	0.2196	161	0.1668	3388	X-RAY DIFFRACTION	100
1.8097-1.8368	0.2054	153	0.1722	3377	X-RAY DIFFRACTION	100
1.8368-1.8655	0.2074	196	0.1706	3311	X-RAY DIFFRACTION	100
1.8655-1.896	0.1933	176	0.1649	3383	X-RAY DIFFRACTION	100
1.896-1.9287	0.1827	196	0.1601	3345	X-RAY DIFFRACTION	100
1.9287-1.9638	0.1816	172	0.1548	3385	X-RAY DIFFRACTION	100
1.9638-2.0016	0.1974	170	0.1586	3352	X-RAY DIFFRACTION	100
2.0016-2.0424	0.1747	176	0.1549	3373	X-RAY DIFFRACTION	100
2.0424-2.0868	0.2019	178	0.1524	3343	X-RAY DIFFRACTION	100
2.0868-2.1354	0.1983	170	0.1574	3398	X-RAY DIFFRACTION	100
2.1354-2.1888	0.1887	187	0.153	3365	X-RAY DIFFRACTION	100
2.1888-2.248	0.1902	181	0.1538	3387	X-RAY DIFFRACTION	100
2.248-2.3141	0.1921	179	0.162	3389	X-RAY DIFFRACTION	100
2.3141-2.3888	0.1753	174	0.1568	3379	X-RAY DIFFRACTION	100
2.3888-2.4742	0.1889	164	0.1522	3393	X-RAY DIFFRACTION	100
2.4742-2.5732	0.1817	195	0.1567	3385	X-RAY DIFFRACTION	100
2.5732-2.6903	0.2162	175	0.1596	3426	X-RAY DIFFRACTION	100
2.6903-2.8321	0.2001	176	0.1674	3379	X-RAY DIFFRACTION	100
2.8321-3.0095	0.1825	179	0.1604	3431	X-RAY DIFFRACTION	100
3.0095-3.2419	0.1708	184	0.1594	3415	X-RAY DIFFRACTION	100
3.2419-3.568	0.1598	180	0.141	3436	X-RAY DIFFRACTION	100
3.568-4.084	0.1326	177	0.1265	3462	X-RAY DIFFRACTION	100
4.084-5.1442	0.1147	190	0.1148	3493	X-RAY DIFFRACTION	100
5.1442-44.8843	0.17	185	0.1563	3505	X-RAY DIFFRACTION	96

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	0.9311	0.333	-0.2017	0.0185	-0.0497	1.2627	0.0208	-0.1818	0.1273	0.0012	-0.031	-0.1045	-0.0965	0.3213	0.0025	0.1367	-0.0197	-0.025	0.2567	-0.0039	0.2157	17.633	9.8804	-9.5524
2	0.7527	0.1952	0.0263	0.3999	0.1309	0.7114	-0.0058	-0.1597	0.0056	0.0482	-0.0205	-0.0636	0.0195	0.1303	0.0224	0.1405	0.0075	-0.0214	0.1879	0.0093	0.1849	6.0957	3.9819	-7.1846
3	0.8318	-0.6793	1.2906	0.9584	-0.3823	1.6954	-0.0502	0.0198	0.5032	0.0484	-0.1092	-0.0146	-0.2555	0.1641	0.1696	0.1824	0.0065	-0.0162	0.172	-0.0332	0.2107	-15.4468	19.0764	-16.4092
4	5.9041	2.0911	-0.3625	5.5868	-1.4071	3.6632	-0.0636	0.0154	0.2846	0.1052	-0.1353	-0.0953	-0.2063	-0.0532	0.1819	0.1197	0.0255	-0.0349	0.1257	-0.0298	0.1189	-21.0706	14.0141	-12.1371
5	0.3389	-0.0709	-0.0597	0.2157	-0.0808	1.7212	-0.0141	-0.0523	0.0697	0.0243	-0.0001	0.0049	-0.1764	0.0216	0.0169	0.1659	-0.0012	-0.0086	0.1473	-0.0006	0.2041	-11.4224	9.8319	-15.097
6	0.8506	0.239	-0.133	1.1908	0.5756	1.131	-0.0353	0.1885	0.1448	-0.2078	-0.0201	0.0478	-0.1831	-0.1818	0.0202	0.1596	0.0167	-0.0358	0.1577	0.0434	0.1492	-19.2411	7.4511	-40.9627
7	1.2917	0.093	-1.3045	0.7967	-0.625	2.1513	-0.2576	0.423	-0.1987	-0.0442	0.1304	0.1372	0.5029	-0.7903	-0.0061	0.2156	-0.1711	0.0352	0.3768	-0.0526	0.205	-35.9337	-17.5242	-26.1838
8	1.4703	0.007	-0.5384	0.787	0.1555	1.343	-0.1787	0.0216	-0.2594	0.2657	-0.0116	0.1027	0.5432	-0.3126	0.0825	0.3493	-0.0944	0.0923	0.2061	-0.0043	0.1933	-30.4627	-21.5179	-9.7602
9	2.3776	-0.5603	-1.9086	0.5019	0.243	1.6053	-0.1658	0.4994	-0.5006	0.1275	0.0077	0.0135	0.5111	-0.1295	0.1896	0.3606	0.0127	0.0448	0.1423	-0.0054	0.2802	-6.5626	-28.7175	-26.702
10	3.8424	1.0313	-0.099	1.4926	0.3462	1.8189	-0.1287	0.2318	-0.4567	0.0437	0.157	-0.1912	0.3138	0.1126	-0.0573	0.3495	0.0615	0.0304	0.1591	0.0001	0.2417	-3.7034	-26.5209	-17.5525
11	0.8321	-0.0546	-0.3822	0.1968	-0.0209	0.9099	-0.085	-0.0053	-0.1703	0.0672	0.0047	-0.0025	0.2585	-0.0435	0.022	0.2238	-0.0054	0.0182	0.093	0.0021	0.1821	-10.1435	-19.9587	-23.8602
12	1.5129	0.2235	0.5083	1.8334	0.4335	1.8244	-0.0251	0.1413	0.0172	-0.1267	0.0367	-0.169	0.0268	0.1533	-0.0241	0.1256	0.0053	0.041	0.1548	0.0093	0.1538	1.9361	-7.0039	-42.3725

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 3 through 76 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 77 through 223 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 224 through 255 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 256 through 283 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 284 through 430 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 431 through 514 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 3 through 139 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 140 through 223 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 224 through 255 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 256 through 294 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 295 through 445 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 446 through 505 )

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