PDB-5dw4: Succinyl-CoA:acetate CoA-transferase (AarCH6) bound to acetate

ID or keywords:

Entry

Database: PDB / ID: 5dw4

Title

Succinyl-CoA:acetate CoA-transferase (AarCH6) bound to acetate

Components

Succinyl-CoA:acetate CoA-transferase

Keywords

TRANSFERASE / Tricarboxylic acid cycle / Acidophile

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: 1.622 Å

Authors

Murphy, J.R. / 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	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

-
Download

PDBx/mmCIF format	5dw4.cif.gz	415.3 KB	Display	PDBx/mmCIF format
PDB format	pdb5dw4.ent.gz	339.5 KB	Display	PDB format
PDBx/mmJSON format	5dw4.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	5dw4_validation.pdf.gz	468 KB	Display	wwPDB validaton report
Full document	5dw4_full_validation.pdf.gz	474 KB	Display
Data in XML	5dw4_validation.xml.gz	46.6 KB	Display
Data in CIF	5dw4_validation.cif.gz	70.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/dw/5dw4 ftp://data.pdbj.org/pub/pdb/validation_reports/dw/5dw4	HTTPS FTP

-
Related structure data

Related structure data	5ddkC 5dw5C 5dw6C 5e5hC 4eu9S 4eu3 C: citing same article (ref.) S: Starting model for refinement
Similar structure data	4eu3-d 5e5h-d 4eu6-d 4eu9-d 4eud-d 5dw5-d 2nvv-2 3qar-d 4kz0-d 3sd5-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

-
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

113 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)	67.503, 110.393, 120.021
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: 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
#2: Chemical	ChemComp-IMD / IMIDAZOLE Mass: 69.085 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C₃H₅N₂
#3: Chemical	ChemComp-ACT / ACETATE ION Mass: 59.044 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₂H₃O₂
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1017 / Source method: isolated from a natural source / Formula: H₂O

-
Experiment

Experiment	Method: X-RAY DIFFRACTION

-
Sample preparation

Crystal	Density Matthews: 1.93 Å³/Da / Density % sol: 36.4 %
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, 50 mM sodium acetate

-
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: 1.62→50 Å / Num. obs: 113965 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 8.4 % / R_sym value: 0.096 / Net I/σ(I): 30.47
Reflection shell	Resolution: 1.62→1.65 Å / Redundancy: 7.7 % / R_merge(I) obs: 0.573 / Mean I/σ(I) obs: 4.02 / R_sym value: 0.573 / % possible all: 100

-
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: 1.622→44.85 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 16.64 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1767	5691	5 %	same as 4eu9
R_work	0.1502	-	-	-
obs	0.1515	113874	99.84 %	-

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.622→44.85 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7763	0	49	1017	8829

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	8112
X-RAY DIFFRACTION	f_angle_d	1.136	11007
X-RAY DIFFRACTION	f_dihedral_angle_d	13.141	3049
X-RAY DIFFRACTION	f_chiral_restr	0.049	1218
X-RAY DIFFRACTION	f_plane_restr	0.006	1475

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 (%)
1.6216-1.6401	0.2492	175	0.1959	3410	X-RAY DIFFRACTION	95
1.6401-1.6594	0.2445	165	0.1844	3578	X-RAY DIFFRACTION	100
1.6594-1.6796	0.2054	198	0.1815	3581	X-RAY DIFFRACTION	100
1.6796-1.7009	0.2044	203	0.1795	3540	X-RAY DIFFRACTION	100
1.7009-1.7232	0.2166	173	0.1698	3603	X-RAY DIFFRACTION	100
1.7232-1.7468	0.2183	198	0.1694	3557	X-RAY DIFFRACTION	100
1.7468-1.7718	0.207	198	0.1686	3571	X-RAY DIFFRACTION	100
1.7718-1.7982	0.2227	190	0.1698	3545	X-RAY DIFFRACTION	100
1.7982-1.8263	0.1818	167	0.1631	3626	X-RAY DIFFRACTION	100
1.8263-1.8563	0.19	183	0.1569	3571	X-RAY DIFFRACTION	100
1.8563-1.8883	0.1821	198	0.1499	3572	X-RAY DIFFRACTION	100
1.8883-1.9226	0.1766	201	0.1495	3586	X-RAY DIFFRACTION	100
1.9226-1.9596	0.1963	182	0.1505	3595	X-RAY DIFFRACTION	100
1.9596-1.9996	0.1957	185	0.1544	3575	X-RAY DIFFRACTION	100
1.9996-2.0431	0.1881	194	0.1545	3590	X-RAY DIFFRACTION	100
2.0431-2.0906	0.1757	190	0.1495	3571	X-RAY DIFFRACTION	100
2.0906-2.1429	0.1729	179	0.151	3604	X-RAY DIFFRACTION	100
2.1429-2.2008	0.1874	196	0.1465	3605	X-RAY DIFFRACTION	100
2.2008-2.2656	0.1649	199	0.1495	3605	X-RAY DIFFRACTION	100
2.2656-2.3387	0.1971	177	0.1535	3600	X-RAY DIFFRACTION	100
2.3387-2.4223	0.1838	193	0.1506	3606	X-RAY DIFFRACTION	100
2.4223-2.5193	0.2018	189	0.1508	3634	X-RAY DIFFRACTION	100
2.5193-2.6339	0.1959	198	0.1635	3600	X-RAY DIFFRACTION	100
2.6339-2.7728	0.1855	178	0.155	3643	X-RAY DIFFRACTION	100
2.7728-2.9465	0.1844	205	0.1566	3628	X-RAY DIFFRACTION	100
2.9465-3.1739	0.1739	190	0.1528	3648	X-RAY DIFFRACTION	100
3.1739-3.4932	0.1475	184	0.1416	3651	X-RAY DIFFRACTION	100
3.4932-3.9984	0.1417	194	0.1223	3699	X-RAY DIFFRACTION	100
3.9984-5.0365	0.126	201	0.1233	3719	X-RAY DIFFRACTION	100
5.0365-44.867	0.172	208	0.1526	3870	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	0.5782	0.1574	0.175	0.1833	-0.0438	0.7032	-0.0108	-0.0936	0.1114	0.003	-0.0045	-0.0607	-0.0845	0.2249	0.0066	0.0712	-0.0164	-0.0132	0.1523	-0.0129	0.1171	17.6736	9.7695	-9.7476
2	0.6101	0.1212	-0.0235	0.2408	0.0967	0.4072	0.0018	-0.1255	0.0284	0.0497	-0.0068	-0.0332	-0.0021	0.0853	0.0027	0.0714	0.008	-0.0142	0.0797	0.0017	0.078	6.1716	4.0501	-7.5383
3	0.7878	-0.3383	1.0483	0.5593	-0.1572	1.4133	-0.1258	0.0418	0.4093	0.0247	-0.0324	0.0444	-0.2051	0.057	0.1615	0.1182	0.0129	-0.0285	0.0827	-0.0257	0.1378	-14.7486	19.1907	-16.4933
4	4.6005	1.6238	-0.2639	3.4822	-1.0609	2.3139	-0.052	0.053	0.164	0.0906	-0.0682	-0.0216	-0.1538	-0.0075	0.1046	0.0685	0.0108	-0.0207	0.079	-0.0131	0.072	-20.9499	13.9839	-12.5143
5	0.3133	-0.0929	0.0287	0.1927	0.0334	1.1326	-0.0176	-0.038	0.0559	0.0089	0.0077	0.0209	-0.1118	0.0056	0.007	0.0819	-0.0046	-0.0099	0.0514	0.0007	0.0973	-11.3938	9.7779	-15.3031
6	0.6424	0.1182	0.0164	0.7541	0.4897	0.6409	-0.0605	0.1762	0.1067	-0.1572	-0.0177	0.066	-0.1503	-0.1091	-0.0403	0.111	0.0078	-0.0403	0.0914	0.0344	0.0983	-19.2052	7.3519	-41.2551
7	0.7885	0.1578	-0.2011	0.3561	-0.2404	0.6911	-0.082	0.1114	-0.0964	-0.0239	0.0462	0.0938	0.1606	-0.2974	-0.0097	0.1234	-0.0635	0.0204	0.1833	-0.031	0.1249	-36.0262	-17.571	-26.0794
8	0.9015	0.2501	0.5852	0.5965	0.3351	0.3834	0.0337	-0.1132	-0.1318	0.1606	-0.0817	0.0948	0.1957	-0.169	0.0368	0.1879	-0.0576	0.0581	0.1557	-0.0017	0.1152	-30.7879	-21.3688	-9.9457
9	1.5358	-0.1583	-0.9296	0.3102	0.0795	0.5374	-0.2919	0.188	-0.4367	0.0236	0.1447	-0.071	0.2696	-0.0781	0.0515	0.2502	0.0223	0.0582	0.0766	0.0127	0.2006	-6.6065	-29.1408	-26.5721
10	2.7786	-0.241	-0.2243	1.1916	-0.1217	1.6618	-0.0927	0.2108	-0.4761	0.1683	0.0973	-0.0882	0.2331	0.0642	-0.0003	0.1947	0.0387	0.0135	0.1024	0.0012	0.2103	-3.5556	-26.8329	-17.5445
11	0.7067	-0.1331	-0.1553	0.2771	0.2808	0.6271	-0.047	0.0039	-0.1431	0.0774	0.0081	0.0342	0.1939	-0.0124	-0.0225	0.1411	-0.0104	0.0112	0.037	0.0059	0.1143	-10.1555	-20.1165	-23.8089
12	1.1822	0.0625	0.3113	1.5176	0.2433	1.3265	-0.011	0.1341	-0.0196	-0.1134	0.015	-0.0906	0.0008	0.1291	-0.0126	0.0612	-0.0004	0.0239	0.0736	0.0016	0.0646	2.0005	-7.2077	-42.6525

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 )

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi