PDB-5dw6: Succinyl-CoA:acetate CoA-transferase (AarCH6) bound to acetate an...

ID or keywords:

Entry

Database: PDB / ID: 5dw6

Title

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

Components

Succinyl-CoA:acetate CoA-transferase

Keywords

TRANSFERASE / Tricarboxylic acid cycle / Acidophile / coenzyme analogue

Function / homology

Function and homology information

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

Biological species

Acetobacter aceti 1023 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

FOURIER SYNTHESIS / Resolution: 1.548 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	Jul 20, 2016	Group: Data collection
Revision 1.3	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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Download

PDBx/mmCIF format	5dw6.cif.gz	418.9 KB	Display	PDBx/mmCIF format
PDB format	pdb5dw6.ent.gz	342.5 KB	Display	PDB format
PDBx/mmJSON format	5dw6.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	5dw6_validation.pdf.gz	919.4 KB	Display	wwPDB validaton report
Full document	5dw6_full_validation.pdf.gz	925.3 KB	Display
Data in XML	5dw6_validation.xml.gz	46 KB	Display
Data in CIF	5dw6_validation.cif.gz	70 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/dw/5dw6 ftp://data.pdbj.org/pub/pdb/validation_reports/dw/5dw6	HTTPS FTP

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Related structure data

Related structure data	5ddkC 5dw4C 5dw5C 5e5hC 4eu9S C: citing same article (ref.) S: Starting model for refinement
Similar structure data	4eu5-d 5dw5-d 4eua-d 5ddk-d 4eu7-d 4euc-d 4eu9-d 2nvv-2 4eub-d 2g39-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)	67.425, 110.455, 120.003
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#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 1023 (bacteria) / 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
#2: Chemical	ChemComp-ACT / ACETATE ION Mass: 59.044 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₂H₃O₂
#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-IMD / IMIDAZOLE Mass: 69.085 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₃H₅N₂
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 939 / 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: 1.93 Å³/Da / Density % sol: 36.4 %
Crystal grow	Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.2 Details: 0.9 M sodium citrate, 0.1 M imidazole, 25 mM 2-mercaptoethanol, 3 mM MX; drops adjusted to 50 mM sodium acetate (pH 8.2 stock) 3 d prior to cryoprotection

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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: 1.548→50 Å / Num. obs: 130308 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 8.1 % / R_sym value: 0.075 / Net I/σ(I): 37.4
Reflection shell	Resolution: 1.548→1.58 Å / Redundancy: 7.8 % / Mean I/σ(I) obs: 3.32 / R_sym value: 0.601 / % possible all: 100

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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: 1.548→44.823 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.63 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1787	6492	4.99 %	Same as 4eu9
R_work	0.1566	-	-	-
obs	0.1577	130205	99.54 %	-

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.548→44.823 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7761	0	135	939	8835

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.009	8174
X-RAY DIFFRACTION	f_angle_d	1.255	11105
X-RAY DIFFRACTION	f_dihedral_angle_d	13.68	3059
X-RAY DIFFRACTION	f_chiral_restr	0.054	1227
X-RAY DIFFRACTION	f_plane_restr	0.006	1473

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 (%)
1.5481-1.5657	0.2372	189	0.21	3586	X-RAY DIFFRACTION	87
1.5657-1.5841	0.2391	218	0.2124	4093	X-RAY DIFFRACTION	100
1.5841-1.6034	0.2462	194	0.2013	4142	X-RAY DIFFRACTION	100
1.6034-1.6237	0.2205	223	0.1958	4063	X-RAY DIFFRACTION	100
1.6237-1.6451	0.2109	205	0.1843	4125	X-RAY DIFFRACTION	100
1.6451-1.6676	0.2022	207	0.1817	4082	X-RAY DIFFRACTION	100
1.6676-1.6914	0.2016	231	0.1793	4101	X-RAY DIFFRACTION	100
1.6914-1.7167	0.2128	204	0.176	4105	X-RAY DIFFRACTION	100
1.7167-1.7435	0.2091	224	0.1744	4103	X-RAY DIFFRACTION	100
1.7435-1.7721	0.2209	232	0.1731	4119	X-RAY DIFFRACTION	100
1.7721-1.8027	0.215	206	0.1728	4067	X-RAY DIFFRACTION	100
1.8027-1.8354	0.1976	194	0.1708	4162	X-RAY DIFFRACTION	100
1.8354-1.8707	0.1962	238	0.169	4092	X-RAY DIFFRACTION	100
1.8707-1.9089	0.1941	208	0.1648	4106	X-RAY DIFFRACTION	100
1.9089-1.9504	0.1836	226	0.1703	4074	X-RAY DIFFRACTION	100
1.9504-1.9958	0.1994	216	0.1661	4168	X-RAY DIFFRACTION	100
1.9958-2.0457	0.1785	217	0.1594	4143	X-RAY DIFFRACTION	100
2.0457-2.101	0.183	225	0.1586	4101	X-RAY DIFFRACTION	100
2.101-2.1629	0.1868	203	0.1555	4135	X-RAY DIFFRACTION	100
2.1629-2.2327	0.2032	223	0.1567	4130	X-RAY DIFFRACTION	100
2.2327-2.3125	0.1901	219	0.1623	4140	X-RAY DIFFRACTION	100
2.3125-2.405	0.1859	218	0.1596	4154	X-RAY DIFFRACTION	100
2.405-2.5145	0.1823	209	0.1576	4156	X-RAY DIFFRACTION	100
2.5145-2.647	0.2037	232	0.1625	4139	X-RAY DIFFRACTION	100
2.647-2.8129	0.2128	204	0.1667	4202	X-RAY DIFFRACTION	100
2.8129-3.03	0.1755	230	0.1604	4144	X-RAY DIFFRACTION	100
3.03-3.3348	0.156	223	0.1542	4211	X-RAY DIFFRACTION	100
3.3348-3.8172	0.1431	216	0.1305	4214	X-RAY DIFFRACTION	100
3.8172-4.8084	0.1285	222	0.1205	4274	X-RAY DIFFRACTION	100
4.8084-44.8419	0.1595	236	0.1497	4382	X-RAY DIFFRACTION	99

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	0.3572	0.1528	0.3825	0.359	0.1254	0.4456	0.0226	-0.196	0.0825	0.0182	-0.0354	-0.0881	-0.0731	0.2346	0.0128	0.1045	-0.0193	-0.0196	0.2644	0.0056	0.1863	17.6251	9.6666	-9.6493
2	0.6819	0.1948	-0.0719	0.2472	0.091	0.4763	-0.008	-0.1852	0.0223	0.0492	-0.0274	-0.068	0.0044	0.1768	0.0273	0.092	0.0095	-0.0218	0.1603	0.0148	0.1306	6.1484	3.9366	-7.2268
3	1.4797	-0.6125	1.0464	0.4496	-0.2361	1.3149	-0.085	-0.0701	0.463	0.0284	-0.0689	0.0207	-0.2297	0.0436	0.1593	0.1481	0.0074	-0.0151	0.1423	-0.0273	0.1725	-15.4724	18.9687	-16.3236
4	4.0589	1.2219	-0.0622	3.4387	-0.7681	2.5653	-0.1072	0.1082	0.2778	-0.0015	-0.0706	-0.0046	-0.208	-0.0502	0.1318	0.1109	0.0115	-0.0328	0.1204	-0.0128	0.1182	-21.0261	13.8722	-12.0811
5	0.451	-0.1201	-0.0949	0.1964	-0.1318	1.577	-0.0214	-0.0576	0.0759	0.0253	-0.0024	-0.012	-0.152	0.0142	0.0176	0.1155	-0.0021	-0.0159	0.0937	-0.0034	0.1471	-11.4839	9.664	-15.0713
6	0.6293	0.0598	-0.0059	0.7444	0.3243	0.511	-0.0287	0.1783	0.1251	-0.1494	-0.0085	0.0258	-0.1275	-0.1513	0.0009	0.1083	0.0102	-0.0209	0.1174	0.0334	0.0954	-19.1738	7.4769	-40.9174
7	0.3999	-0.1016	-0.0824	0.2103	0.207	0.6181	-0.2788	0.3398	-0.1728	0.0189	0.0607	0.1609	0.5116	-0.7811	-0.4933	0.1569	-0.323	0.1188	0.3863	-0.0602	0.1889	-35.9359	-17.8599	-26.0794
8	0.0949	-0.0164	-0.0239	0.4824	0.2232	0.4221	-0.1903	0.002	-0.2229	0.2211	-0.0234	0.1002	0.5452	-0.3406	-0.5657	0.3676	-0.1548	0.1445	0.2038	-0.009	0.1785	-30.4245	-21.6628	-9.8116
9	0.5843	-0.2926	-0.6451	0.5164	-0.0626	1.1046	-0.1524	0.144	-0.2138	0.0669	-0.0763	0.1008	0.4338	-0.1093	0.1049	0.3412	0.0323	0.0755	0.1397	-0.0391	0.2584	-6.5163	-28.8518	-26.7184
10	2.9702	0.5363	0.0078	1.0751	-0.9116	1.2126	-0.0421	0.294	-0.3251	0.0246	0.0986	-0.1041	0.2478	0.0283	-0.0799	0.3107	0.071	0.0225	0.1456	-0.0076	0.2001	-3.6263	-26.625	-17.6363
11	0.3772	-0.0973	-0.0343	0.2449	-0.053	0.1922	-0.0566	0.0145	-0.1215	0.0615	0.0214	-0.0041	0.221	-0.0185	-0.0264	0.2065	-0.0047	0.0252	0.0841	0.0068	0.1482	-10.0602	-20.0891	-23.8526
12	1.436	0.4272	0.4066	1.6517	0.573	1.6711	-0.0201	0.1207	0.002	-0.106	0.0195	-0.1599	0.063	0.156	-0.0078	0.0833	0.0147	0.0389	0.1051	0.0168	0.1042	2.0848	-6.7447	-42.1939

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 2 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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