PDB-9eir: Ethylene-forming enzyme apoprotein from Penicillium digitatum

ID or keywords:

Entry

Database: PDB / ID: 9eir

Title

Ethylene-forming enzyme apoprotein from Penicillium digitatum

Components

2-oxoglutarate-dependent ethylene/succinate-forming enzyme

Keywords

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

Function / homology

Function and homology information

small molecule biosynthetic process / oxidoreductase activity / metal ion binding
Similarity search - Function

Biological species

Penicillium digitatum Pd1 (fungus)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 3.5 Å

Authors

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

Funding support

United States, 2items

Citation

Journal: Biochemistry / Year: 2025
Title: Biochemical, Structural, and Conformational Characterization of a Fungal Ethylene-Forming Enzyme.
Authors: Chatterjee, S. / Rankin, J.A. / Farrugia, M.A. / J S Rifayee, S.B. / Christov, C.Z. / Hu, J. / Hausinger, R.P.

History

Deposition	Nov 26, 2024	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Apr 2, 2025	Provider: repository / Type: Initial release
Revision 1.1	May 14, 2025	Group: Database references / Category: citation Item: _citation.journal_volume / _citation.page_first / _citation.page_last

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	9eir.cif.gz	486.3 KB	Display	PDBx/mmCIF format
PDB format	pdb9eir.ent.gz	399.7 KB	Display	PDB format
PDBx/mmJSON format	9eir.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ei/9eir ftp://data.pdbj.org/pub/pdb/validation_reports/ei/9eir	HTTPS FTP

-
Related structure data

Related structure data	9eisC C: citing same article (ref.)
Similar structure data	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	#240 - Dec 2019 Hypoxia-Inducible Factors similarity (2)

Deposited unit

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

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

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

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

183 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

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

defined by author&software
Evidence: gel filtration, In SEC it is predominantly monomer
45.8 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

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

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

3

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

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

4

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

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

Unit cell

Length a, b, c (Å)	101.599, 115.880, 142.050
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	2-oxoglutarate-dependent ethylene/succinate-forming enzyme Mass: 45806.812 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Penicillium digitatum Pd1 (fungus) / Gene: Pdw03_5776 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A7T7BQH3
Has protein modification	N

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.28 Å³/Da / Density % sol: 46.1 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, sitting drop Details: 10 % PEG 8000, 100 mM imidazole-HCl (pH 8.0), and 200 mM calcium acetate

-
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: Sep 21, 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: 3.5→89.79 Å / Num. obs: 21668 / % possible obs: 99.6 % / Redundancy: 6.2 % / CC_1/2: 0.947 / Net I/σ(I): 5.1
Reflection shell	Resolution: 3.5→3.78 Å / Num. unique obs: 4376 / CC_1/2: 0.594

-
Processing

Software

Name	Version	Classification
PHENIX	1.19_4092	refinement
iMOSFLM		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 3.5→89.79 Å / SU ML: 0.55 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 30.52 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2781	1903	4.73 %
R_work	0.242	-	-
obs	0.2438	40246	98.58 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 3.5→89.79 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	9361	0	0	0	9361

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.001	9649
X-RAY DIFFRACTION	f_angle_d	0.431	13244
X-RAY DIFFRACTION	f_dihedral_angle_d	10.214	3270
X-RAY DIFFRACTION	f_chiral_restr	0.041	1494
X-RAY DIFFRACTION	f_plane_restr	0.004	1725

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 (%)
3.5-3.59	0.3088	113	0.3659	2737	X-RAY DIFFRACTION	98
3.59-3.68	0.3611	154	0.334	2724	X-RAY DIFFRACTION	99
3.68-3.79	0.3763	113	0.3115	2709	X-RAY DIFFRACTION	97
3.79-3.92	0.3216	150	0.2937	2672	X-RAY DIFFRACTION	96
3.92-4.06	0.305	113	0.2841	2793	X-RAY DIFFRACTION	99
4.06-4.22	0.2699	128	0.2599	2748	X-RAY DIFFRACTION	100
4.22-4.41	0.3191	150	0.2399	2762	X-RAY DIFFRACTION	99
4.41-4.64	0.2869	124	0.2223	2775	X-RAY DIFFRACTION	99
4.64-4.93	0.2553	128	0.2053	2741	X-RAY DIFFRACTION	99
4.93-5.31	0.2483	155	0.2103	2767	X-RAY DIFFRACTION	99
5.31-5.85	0.2692	134	0.2363	2767	X-RAY DIFFRACTION	100
5.85-6.69	0.2864	169	0.224	2742	X-RAY DIFFRACTION	99
6.7-8.43	0.2232	120	0.2127	2679	X-RAY DIFFRACTION	97
8.43-89.79	0.2147	152	0.179	2727	X-RAY DIFFRACTION	98

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	0.4109	0.2562	0.3714	4.7299	-0.0131	0.2992	0.1321	-0.1562	0.495	0.8593	-0.4167	0.3138	-0.4511	0.159	0.2983	0.9649	0.1304	-0.0779	0.7085	-0.1685	0.7315	-29.1631	-17.2511	-11.685
2	2.4145	-0.618	-0.9789	0.2471	0.1525	0.4981	-0.0967	-1.2992	0.2284	0.3888	-0.0375	0.5844	-0.1502	-0.7105	0.0745	0.8758	0.1209	0.0943	1.2007	-0.0109	0.6732	-26.0883	-33.8458	-6.0791
3	1.9068	-0.6192	-1.055	3.6735	-0.3036	0.6864	0.2269	0.3194	-0.1127	-0.2517	-0.3063	-0.225	-0.2122	0.3219	0.1201	0.5904	0.1235	-0.1706	0.6967	-0.0304	0.6268	19.1435	-20.8016	-27.9683
4	1.0903	-0.8263	-0.506	1.8756	-0.111	2.4359	0.1492	-0.2102	-0.2247	0.4368	0.0245	0.252	-0.3359	-0.2774	-0.1147	0.366	0.0367	0.0009	0.6787	0.0448	0.7141	11.0781	-20.326	-19.0827
5	5.9649	7.3011	0.3439	9.0464	0.239	0.7174	0.5619	-0.7698	0.6202	1.1997	-0.5815	-0.1387	-0.323	0.8413	0.0587	0.8084	-0.0176	0.1586	0.8723	0.0415	0.7695	26.0763	-16.9155	-22.2802
6	2.063	0.9242	-0.0051	1.3534	-0.1811	2.466	0.2506	-0.1335	-0.4544	0.5113	-0.1644	-0.2745	-0.0844	0.0628	-0.103	0.8015	0.0063	-0.1215	0.5347	0.1047	0.6871	20.0612	-26.8921	-15.0314
7	2.5358	1.4312	-0.4283	3.4997	-0.1692	4.2096	0.314	0.6616	-0.4881	-0.7623	-0.2169	0.0066	0.64	0.2308	-0.1836	0.8961	0.0663	-0.1517	0.6344	-0.0345	0.7395	-8.6061	-12.9897	-57.8461
8	2.2851	1.2269	0.9959	2.763	0.5191	2.0308	-0.0503	0.1434	0.0666	-0.3403	0.0971	-0.1711	0.2663	0.2153	-0.0633	0.5249	0.0389	-0.0112	0.4076	0.0689	0.4767	4.6042	4.3586	-52.6196
9	8.3544	-1.6242	-3.1391	2.8136	-0.1482	1.9991	0.0893	1.1152	0.2763	0.0193	0.6499	-0.2642	1.5147	0.3716	-0.5643	1.0317	-0.0468	-0.1082	0.706	-0.2772	0.886	5.6202	-9.1554	-57.4602
10	1.4176	0.3768	1.8208	1.5406	1.3907	2.7503	0.2265	0.0304	-0.1725	-0.0336	-0.1319	0.0935	0.473	-0.0794	-0.0734	0.7789	0.0144	0.0252	0.5065	0.0583	0.6056	3.6026	-6.0678	-44.2296
11	2.0804	1.3567	-0.4713	1.2411	-0.8525	1.152	0.2251	0.3118	0.0644	-0.9471	-0.1712	-0.3381	0.4369	0.0093	-0.1123	0.6689	0.1792	0.1358	0.6629	-0.0367	0.6554	18.0051	-49.5358	-80.928
12	0.7043	0.5723	-0.6189	0.3523	-0.3232	1.4133	0.1054	0.1813	0.0464	0.135	0.1154	-0.058	0.1545	-0.1525	-0.1882	0.5065	0.1358	0.0573	0.566	0.0169	0.6788	4.9272	-57.3352	-66.2972
13	3.0944	1.5951	0.923	1.2488	0.5594	1.5136	0.7376	0.4615	0.3777	0.0511	-0.4408	0.2235	-0.0283	0.1747	-0.2373	0.8242	0.1396	0.1162	0.6387	0.0163	0.7692	11.8777	-47.7547	-69.4892
14	0.7421	-0.1367	-0.8176	0.8165	-0.4369	2.577	0.1629	0.1521	0.2688	-0.3046	-0.0884	-0.2746	-0.7613	-0.0683	-0.1197	0.8454	0.0937	0.1614	0.6317	-0.0026	0.6954	8.7283	-43.4397	-68.6938
15	2.741	-0.6122	-0.1707	3.8054	0.7987	2.6093	-0.1917	-0.1127	0.4666	-0.2372	0.542	-0.2276	-0.6374	-0.581	-0.2394	0.5571	0.1212	0.066	0.7992	0.0436	0.7256	-33.1525	-15.4059	-29.9842
16	2.1876	-0.6621	2.3091	3.9294	2.0551	6.8098	0.2917	-0.1911	-0.4792	0.0559	-0.0052	-0.0376	0.7631	-0.6995	-0.2	0.7999	-0.0357	0.2982	0.7029	0.1474	0.758	-30.564	-43.1408	-24.5405
17	2.1321	-1.3802	-0.1776	2.0415	-0.649	3.3221	-0.2439	-0.548	0.3224	0.5432	0.5278	-0.4665	0.0492	0.1289	-0.231	0.5658	0.1336	-0.0525	0.6651	-0.1513	0.6505	-21.4154	-24.4886	-19.7055
18	3.383	0.0122	0.8056	1.3411	-0.0327	0.1807	0.0331	-0.3727	0.3878	0.5742	0.2344	0.3914	-0.1788	-0.6965	-0.3591	0.7278	0.2204	0.0617	0.9633	0.0235	0.7076	-39.2195	-20.2581	-23.628

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'C' and (resid 336 through 368 )
2	X-RAY DIFFRACTION	2	chain 'C' and (resid 369 through 405 )
3	X-RAY DIFFRACTION	3	chain 'D' and (resid 50 through 136 )
4	X-RAY DIFFRACTION	4	chain 'D' and (resid 137 through 232 )
5	X-RAY DIFFRACTION	5	chain 'D' and (resid 233 through 267 )
6	X-RAY DIFFRACTION	6	chain 'D' and (resid 268 through 406 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 48 through 98 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 99 through 232 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 233 through 267 )
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 268 through 407 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 50 through 116 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 117 through 208 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 209 through 256 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 257 through 406 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 48 through 116 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 117 through 150 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 151 through 232 )
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 233 through 335 )

-
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