PDB-9ovh: Structure of an ancestral ethylene forming enzyme, Anc357, in com...

ID or keywords:

Entry

Database: PDB / ID: 9ovh

Title

Structure of an ancestral ethylene forming enzyme, Anc357, in complex with Mn

Components

2-oxoglutarate-dependent ethylene/succinate-forming enzyme

Keywords

OXIDOREDUCTASE / 2-oxoglutarate-dependent ethylene/succinate-forming enzyme

Function / homology

:

Function and homology information

Biological species

unidentified (others)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.15 Å

Authors

Chatterjee, S. / Rankin, J.A. / Farrugia, M.A. / Hu, J. / Hausinger, R.P.

Funding support

United States, 1items

Citation

Journal: Biochemistry / Year: 2025
Title: Ancestral Sequence Reconstruction of the Ethylene-Forming Enzyme.
Authors: Chatterjee, S. / Rankin, J.A. / Farrugia, M.A. / Delaney, B.J. / Pascual, N.S. / VanAntwerp, J. / Woldring, D.R. / Hu, J. / Hausinger, R.P.

History

Deposition	May 30, 2025	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Aug 27, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	9ovh.cif.gz	241.4 KB	Display	PDBx/mmCIF format
PDB format	pdb9ovh.ent.gz	193.1 KB	Display	PDB format
PDBx/mmJSON format	9ovh.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9ovh_validation.pdf.gz	1.2 MB	Display	wwPDB validaton report
Full document	9ovh_full_validation.pdf.gz	1.2 MB	Display
Data in XML	9ovh_validation.xml.gz	27.9 KB	Display
Data in CIF	9ovh_validation.cif.gz	37.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ov/9ovh ftp://data.pdbj.org/pub/pdb/validation_reports/ov/9ovh	HTTPS FTP

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Related structure data

Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: 2-oxoglutarate-dependent ethylene/succinate-forming enzyme

B: 2-oxoglutarate-dependent ethylene/succinate-forming enzyme

hetero molecules

74.6 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: 2-oxoglutarate-dependent ethylene/succinate-forming enzyme

hetero molecules

defined by software
Evidence: gel filtration
37.3 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: 2-oxoglutarate-dependent ethylene/succinate-forming enzyme

hetero molecules

defined by software
37.3 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	39.588, 87.470, 85.492
Angle α, β, γ (deg.)	90.00, 95.43, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	2-oxoglutarate-dependent ethylene/succinate-forming enzyme Mass: 37233.832 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) unidentified (others) / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Chemical	ChemComp-MN / MANGANESE (II) ION Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 250 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y
Has protein modification	N

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 1.98 Å³/Da / Density % sol: 37.84 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, sitting drop Details: 25 % PEG 3350, 100 mM HEPES (pH 7.5), and 200 mM sodium chloride

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.127 Å
Detector	Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Mar 18, 2022
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.127 Å / Relative weight: 1
Reflection	Resolution: 2.15→87.65 Å / Num. obs: 31511 / % possible obs: 100 % / Redundancy: 3.7 % / CC_1/2: 0.993 / Net I/σ(I): 4.9
Reflection shell	Resolution: 2.16→2.23 Å / Num. unique obs: 2758 / CC_1/2: 0.572

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Processing

Software

Name	Version	Classification
PHENIX	(1.19_4092: ???)	refinement
PDB_EXTRACT		data extraction
iMOSFLM		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.15→42.55 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 26.15 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2262	1999	6.76 %
R_work	0.1968	-	-
obs	0.1987	29577	93.78 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.15→42.55 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4480	0	2	250	4732

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	4616
X-RAY DIFFRACTION	f_angle_d	1.016	6281
X-RAY DIFFRACTION	f_dihedral_angle_d	14.044	1659
X-RAY DIFFRACTION	f_chiral_restr	0.062	661
X-RAY DIFFRACTION	f_plane_restr	0.008	843

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 (%)
2.15-2.21	0.3358	104	0.2847	1446	X-RAY DIFFRACTION	68
2.21-2.27	0.3271	117	0.268	1606	X-RAY DIFFRACTION	77
2.27-2.33	0.2916	127	0.2536	1739	X-RAY DIFFRACTION	83
2.33-2.41	0.2783	134	0.2528	1848	X-RAY DIFFRACTION	89
2.41-2.49	0.2835	147	0.2511	2038	X-RAY DIFFRACTION	96
2.49-2.59	0.2808	151	0.2447	2079	X-RAY DIFFRACTION	100
2.59-2.71	0.2608	149	0.2351	2065	X-RAY DIFFRACTION	100
2.71-2.85	0.2581	154	0.2303	2116	X-RAY DIFFRACTION	100
2.85-3.03	0.2499	152	0.214	2089	X-RAY DIFFRACTION	100
3.03-3.27	0.2137	152	0.2036	2102	X-RAY DIFFRACTION	100
3.27-3.6	0.2344	152	0.1804	2107	X-RAY DIFFRACTION	100
3.6-4.12	0.1718	152	0.1565	2084	X-RAY DIFFRACTION	100
4.12-5.18	0.149	153	0.1404	2117	X-RAY DIFFRACTION	100
5.19-42.55	0.2294	155	0.1851	2142	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	1.1194	-0.7824	-0.3777	2.3941	1.0755	1.5958	-0.0723	-0.0205	-0.3927	0.2586	-0.1149	0.1863	0.1221	-0.1283	0.1582	0.2207	-0.0184	0.0273	0.2219	0.009	0.3504	5.0763	27.2872	49.19
2	1.6566	-0.3588	0.0478	2.7875	0.4139	1.4086	-0.0833	-0.0022	-0.0131	-0.0384	0.0152	0.2271	-0.0811	-0.1033	0.0768	0.1689	-0.0355	0.0042	0.1981	0.0133	0.285	6.7501	56.2153	42.8941
3	0.9403	0.5765	-0.3802	2.0542	-0.5222	0.204	-0.1101	0.0888	-0.0082	-0.2847	0.1056	-0.2882	0.02	0.0271	0.0003	0.2163	-0.0018	0.0211	0.2151	-0.0017	0.291	10.5304	40.7462	35.4411
4	1.6908	0.1346	0.1558	1.9482	0.0464	1.4305	-0.2213	-0.1913	0.0026	0.0849	0.1151	0.4739	-0.0706	-0.1205	0.0788	0.2276	0.0377	0.0251	0.2566	0.0444	0.4408	-1.6361	49.4024	45.831
5	2.6658	0.2191	1.371	0.7606	-0.1443	1.812	-0.14	-0.2732	0.2124	0.0756	-0.0702	0.251	-0.1348	-0.2418	0.3566	0.2736	0.03	0.0152	0.2582	-0.0099	0.4205	-3.2068	36.8603	47.1758
6	1.158	0.8199	0.8776	1.5391	0.0614	1.2214	-0.2961	0.077	0.1819	-0.2373	0.1556	0.1767	-0.161	-0.1387	0.2209	0.2904	0.0123	-0.0351	0.295	0.0467	0.3162	-3.7856	41.7962	35.0078
7	2.5479	0.4058	0.2399	1.7125	-0.5338	1.7533	-0.0653	-0.0432	0.3136	0.0626	-0.0012	-0.0968	-0.1032	0.0339	0.0309	0.2257	-0.0029	-0.0099	0.2043	-0.0351	0.3032	10.7362	56.1811	6.5214
8	1.2352	-0.1108	-0.0487	3.0273	-0.1769	1.2238	-0.1131	-0.0328	-0.3609	0.0451	0.0294	0.003	0.2071	0.0527	0.0756	0.2064	-0.0389	0.0076	0.2714	-0.0002	0.4293	5.8614	26.3368	2.1696
9	1.9869	-0.7429	-0.186	2.5675	-1.0158	1.8843	0.0519	0.1268	0.0651	-0.1057	-0.0467	-0.2921	-0.0419	0.1306	-0.028	0.2272	-0.0278	0.0342	0.2429	-0.0371	0.4083	13.13	28.8299	-3.2153
10	3.3516	0.0134	-0.6935	1.3763	-0.3761	3.9032	-0.0619	0.3966	0.0382	-0.0714	0.1373	0.0372	-0.1427	-0.2888	-0.0554	0.2018	-0.0023	0.0073	0.2238	-0.0143	0.3851	3.1427	29.58	-10.1236
11	2.1767	0.918	0.2472	3.6718	0.0218	0.5494	-0.1371	0.2934	0.105	-0.3126	0.1701	0.2946	-0.0456	-0.0547	-0.001	0.2315	0.0038	-0.0121	0.2131	0.0149	0.2132	6.3441	49.1905	-5.3912
12	1.4927	0.1299	0.8955	2.861	-0.1039	0.7814	-0.1113	-0.0472	0.1702	0.0338	0.0232	-0.302	-0.0162	0.1732	0.0944	0.2382	0.0377	0.0338	0.2907	0.0098	0.401	16.3837	37.4675	5.2418
13	1.0777	0.5226	-0.7718	2.1774	0.0154	0.6846	-0.2077	-0.1471	-0.0981	-0.0538	-0.0214	-0.5206	0.0998	0.1647	0.2154	0.2337	0.031	0.0145	0.3054	-0.0049	0.4383	18.8513	45.0585	4.4894
14	5.4985	1.7433	-0.2346	1.04	0.2531	0.2374	-0.2522	0.6343	0.8301	-0.4176	0.7498	-0.0614	-0.359	0.4706	-0.015	0.6987	-0.1256	0.0685	0.4501	0.0003	0.4011	20.6163	50.3893	-15.5187
15	1.8932	-1.1332	0.5852	0.7752	-0.8249	2.4825	0.2348	0.0367	-0.328	-0.5476	0.2458	-0.1162	0.4942	1.1743	-0.4557	0.6688	0.1013	0.0869	0.541	-0.1001	0.5511	20.161	32.219	-11.1024

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 8 through 48 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 49 through 113 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 114 through 176 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 177 through 205 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 206 through 256 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 257 through 328 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 9 through 48 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 49 through 86 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 87 through 113 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 114 through 134 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 135 through 176 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 177 through 220 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 221 through 275 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 276 through 312 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 313 through 329 )

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