PDB-5e5h: Succinyl-CoA:acetate CoA-transferase (AarCH6) bound to acetate an...

ID or keywords:

Entry

Database: PDB / ID: 5e5h

Title

Succinyl-CoA:acetate CoA-transferase (AarCH6) bound to acetate and degradation products from the acetyl-CoA analogue dethiaacetyl-CoA

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 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

FOURIER SYNTHESIS / Resolution: 2.052 Å

Authors

Mullins, E.A. / Kappock, T.J.

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	Oct 8, 2015	Deposition site: RCSB / Processing site: RCSB
Supersession	May 18, 2016	ID: 4FAC
Revision 1.0	May 18, 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	5e5h.cif.gz	411.7 KB	Display	PDBx/mmCIF format
PDB format	pdb5e5h.ent.gz	336.2 KB	Display	PDB format
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Validation report

Summary document	5e5h_validation.pdf.gz	1002.4 KB	Display	wwPDB validaton report
Full document	5e5h_full_validation.pdf.gz	1006.9 KB	Display
Data in XML	5e5h_validation.xml.gz	41.8 KB	Display
Data in CIF	5e5h_validation.cif.gz	61.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/e5/5e5h ftp://data.pdbj.org/pub/pdb/validation_reports/e5/5e5h	HTTPS FTP

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Related structure data

Related structure data	5ddkC 5dw4C 5dw5C 5dw6C 4eu9S C: citing same article (ref.) S: Starting model for refinement
Similar structure data	4eu3-d 4eu9-d 4eud-d 5dw4-d 2nvv-2 4eu5-d 1ft1-d 4eua-d 4eu6-d 5dw6-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)	67.192, 109.844, 119.682
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: 56062.289 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

#1: Protein

Succinyl-CoA:acetate CoA-transferase

Mass: 56062.289 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

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Non-polymers , 7 types, 611 molecules

#2: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 4 / 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-ACE / ACETYL GROUP Mass: 44.053 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₄O
#5: Chemical	ChemComp-FMT / FORMIC ACID Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH₂O₂
#6: Chemical	ChemComp-IMD / IMIDAZOLE Mass: 69.085 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₃H₅N₂
#7: Chemical	ChemComp-ACT / ACETATE ION Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₃O₂
#8: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 598 / 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: 1.91 Å³/Da / Density % sol: 35.6 %
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, 10 mM dethiaacetyl-CoA

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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 23, 2011
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: 2.05→50 Å / Num. obs: 55051 / % possible obs: 98 % / Observed criterion σ(I): -3 / Redundancy: 13.3 % / R_sym value: 0.125 / Net I/σ(I): 24.4
Reflection shell	Resolution: 2.05→2.09 Å / Redundancy: 12.7 % / Mean I/σ(I) obs: 4.4 / R_sym value: 0.64 / % possible all: 97.3

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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: 2.052→41.393 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 20.31 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1937	2740	4.99 %	same as 4fac
R_work	0.1511	-	-	-
obs	0.1533	54907	97.8 %	-

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.052→41.393 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7749	0	125	598	8472

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.013	8108
X-RAY DIFFRACTION	f_angle_d	1.376	10999
X-RAY DIFFRACTION	f_dihedral_angle_d	13.967	3015
X-RAY DIFFRACTION	f_chiral_restr	0.058	1212
X-RAY DIFFRACTION	f_plane_restr	0.008	1459

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 (%)
2.0521-2.0875	0.2379	132	0.1802	2552	X-RAY DIFFRACTION	96
2.0875-2.1254	0.2084	126	0.1718	2515	X-RAY DIFFRACTION	97
2.1254-2.1663	0.2319	135	0.1675	2573	X-RAY DIFFRACTION	97
2.1663-2.2105	0.2603	134	0.1627	2527	X-RAY DIFFRACTION	97
2.2105-2.2586	0.2234	141	0.1715	2555	X-RAY DIFFRACTION	96
2.2586-2.3111	0.2208	131	0.1755	2536	X-RAY DIFFRACTION	97
2.3111-2.3689	0.24	136	0.1611	2553	X-RAY DIFFRACTION	97
2.3689-2.433	0.2296	125	0.1571	2542	X-RAY DIFFRACTION	97
2.433-2.5045	0.2149	137	0.1604	2547	X-RAY DIFFRACTION	96
2.5045-2.5854	0.2289	135	0.1593	2557	X-RAY DIFFRACTION	96
2.5854-2.6778	0.2305	136	0.1659	2571	X-RAY DIFFRACTION	98
2.6778-2.7849	0.2458	127	0.1677	2589	X-RAY DIFFRACTION	97
2.7849-2.9117	0.2081	147	0.1644	2609	X-RAY DIFFRACTION	98
2.9117-3.0651	0.2005	140	0.1681	2658	X-RAY DIFFRACTION	100
3.0651-3.2571	0.1946	141	0.1579	2643	X-RAY DIFFRACTION	100
3.2571-3.5085	0.2024	138	0.148	2682	X-RAY DIFFRACTION	100
3.5085-3.8613	0.1577	140	0.1302	2670	X-RAY DIFFRACTION	99
3.8613-4.4195	0.1519	143	0.1169	2698	X-RAY DIFFRACTION	100
4.4195-5.5659	0.1395	147	0.1275	2723	X-RAY DIFFRACTION	100
5.5659-41.4018	0.161	149	0.1501	2867	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	0.9691	0.3735	0.3248	0.2868	-0.0446	0.7699	-0.0091	-0.1374	0.162	0.0624	-0.0362	-0.0966	-0.1195	0.3215	0.0292	0.1201	-0.032	-0.0291	0.2567	-0.0001	0.207	17.5589	9.9309	-9.3236
2	1.0431	0.1382	0.0235	0.4473	0.0562	0.9296	0.0057	-0.187	0.0034	0.0719	-0.0366	-0.0527	0.0124	0.1785	0.0265	0.1005	0.0057	-0.0099	0.1447	0.0126	0.1418	6.1379	3.9269	-7.319
3	1.7279	-0.715	1.9926	0.3421	-0.5423	2.4908	-0.1484	0.1298	0.6238	0.0322	-0.0525	0.0559	-0.2474	0.1291	0.1929	0.1685	0.0359	-0.0227	0.1605	-0.048	0.2382	-15.3334	18.9716	-16.5691
4	5.9285	1.6428	0.1866	5.8682	-1.2952	4.0653	-0.1321	0.2226	0.4408	0.0647	-0.1501	-0.0468	-0.3727	0.0055	0.2498	0.1468	0.0143	-0.0501	0.1658	-0.0012	0.1419	-20.9443	13.8814	-12.3142
5	0.5255	-0.1622	-0.0254	0.152	0.0837	2.1443	-0.0185	-0.0563	0.0907	0.0257	-0.0035	-0.0055	-0.1623	0.0146	0.0177	0.1131	-0.0137	-0.0157	0.105	0.0063	0.1643	-11.4353	9.7469	-15.0934
6	0.997	0.1993	-0.2477	0.9558	0.4793	0.8678	-0.0617	0.204	0.1263	-0.1531	-0.0151	0.0567	-0.1033	-0.1564	0.0363	0.1302	0.0094	-0.0408	0.1587	0.0442	0.1397	-18.9629	7.1713	-40.5595
7	1.1837	0.1668	-0.7715	0.5107	-0.6081	1.1232	-0.2265	0.3674	-0.1496	-0.0073	0.0755	0.1604	0.4994	-0.7115	-0.0325	0.2277	-0.235	0.0662	0.4167	-0.0806	0.2064	-35.9272	-17.7282	-25.9629
8	1.3894	0.5951	-0.512	1.1199	0.2291	0.86	-0.218	-0.0781	-0.1762	0.2769	-0.0117	0.1272	0.5199	-0.3381	0.0286	0.3758	-0.1295	0.1036	0.2469	-0.0113	0.1817	-30.4344	-21.5017	-9.7506
9	1.335	-0.4654	-1.0689	0.3303	0.1398	1.0779	-0.5238	0.4368	-0.6221	0.1681	0.1401	0.0715	0.7765	-0.1234	0.1958	0.413	0.0505	0.1205	0.0743	0.0105	0.3098	-6.4725	-29.077	-26.5209
10	5.7287	0.8602	-1.0759	2.7576	-0.2444	1.6804	-0.2013	0.4373	-0.4668	0.2718	0.2195	-0.072	0.2684	0.1649	-0.0293	0.3405	0.0617	0.0193	0.1454	-0.0016	0.2069	-3.5195	-26.5961	-17.4148
11	0.7729	-0.0389	-0.2261	0.4378	0.2766	0.6967	-0.0675	0.0225	-0.1904	0.1198	-0.0224	0.0256	0.319	-0.0146	0.0103	0.2327	-0.009	0.0298	0.073	0.005	0.1844	-10.0601	-20.1011	-23.6642
12	1.3972	0.5797	0.7125	1.8969	0.5444	1.4971	-0.0416	0.1649	-0.0282	-0.1248	0.0384	-0.1727	0.0249	0.2093	-0.0104	0.0922	0.0057	0.0377	0.1489	0.0088	0.1259	2.0235	-7.0813	-42.3438

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 2 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 512 )
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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