PDB-9eis: Ethylene forming enzyme in complex with manganese and 2-oxoglutar...

ID or keywords:

Entry

Database: PDB / ID: 9eis

Title

Ethylene forming enzyme in complex with manganese and 2-oxoglutarate 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: 2.8 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

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Download

PDBx/mmCIF format	9eis.cif.gz	517.4 KB	Display	PDBx/mmCIF format
PDB format	pdb9eis.ent.gz	425 KB	Display	PDB format
PDBx/mmJSON format	9eis.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9eis_validation.pdf.gz	923.5 KB	Display	wwPDB validaton report
Full document	9eis_full_validation.pdf.gz	952.3 KB	Display
Data in XML	9eis_validation.xml.gz	58.7 KB	Display
Data in CIF	9eis_validation.cif.gz	75.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ei/9eis ftp://data.pdbj.org/pub/pdb/validation_reports/ei/9eis	HTTPS FTP

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Related structure data

Related structure data	9eirC C: citing same article (ref.)
Similar structure data	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	#240 - Dec 2019 Hypoxia-Inducible Factors similarity (3) #129 - Sep 2010 Isocitrate Dehydrogenase similarity (1)

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

hetero molecules

184 kDa, 4 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 author&software
Evidence: gel filtration
46 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 author&software
45.9 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

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

hetero molecules

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

4

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

hetero molecules

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

Unit cell

Length a, b, c (Å)	104.159, 117.400, 140.740
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, 4 molecules ABCD

#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

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Non-polymers , 5 types, 321 molecules

#2: Chemical	ChemComp-AKG / 2-OXOGLUTARIC ACID Mass: 146.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₅H₆O₅ / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-MN / MANGANESE (II) ION Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#4: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₆O₂
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 312 / Source method: isolated from a natural source / Formula: H₂O

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Details

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: 2.35 Å³/Da / Density % sol: 47.62 %
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 and soaked overnight with 1 mM MnCl2 and 2OG

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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: 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: 2.8→90.1 Å / Num. obs: 43000 / % possible obs: 99.5 % / Redundancy: 6.7 % / CC_1/2: 0.949 / Net I/σ(I): 5.5
Reflection shell	Resolution: 2.8→2.91 Å / Mean I/σ(I) obs: 1.7 / Num. unique obs: 4494 / CC_1/2: 0.352

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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: 2.8→22.85 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 27.51 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2865	2082	4.86 %
R_work	0.2499	-	-
obs	0.2517	42805	99.32 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.8→22.85 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	9916	0	30	312	10258

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.019	10233
X-RAY DIFFRACTION	f_angle_d	1.56	13945
X-RAY DIFFRACTION	f_dihedral_angle_d	15.284	3672
X-RAY DIFFRACTION	f_chiral_restr	0.096	1518
X-RAY DIFFRACTION	f_plane_restr	0.009	1835

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 (%)
2.8-2.86	0.3506	130	0.3243	2710	X-RAY DIFFRACTION	100
2.87-2.94	0.3162	143	0.3182	2662	X-RAY DIFFRACTION	100
2.94-3.02	0.2945	139	0.3019	2703	X-RAY DIFFRACTION	100
3.02-3.1	0.3036	136	0.3033	2668	X-RAY DIFFRACTION	100
3.1-3.2	0.3642	150	0.3069	2696	X-RAY DIFFRACTION	100
3.2-3.32	0.3314	138	0.2978	2680	X-RAY DIFFRACTION	100
3.32-3.45	0.2849	140	0.2681	2722	X-RAY DIFFRACTION	100
3.45-3.61	0.2752	137	0.2439	2582	X-RAY DIFFRACTION	95
3.61-3.8	0.2436	133	0.2443	2730	X-RAY DIFFRACTION	100
3.8-4.03	0.3178	129	0.2355	2735	X-RAY DIFFRACTION	100
4.03-4.34	0.2477	133	0.2128	2744	X-RAY DIFFRACTION	100
4.34-4.78	0.2643	134	0.2033	2744	X-RAY DIFFRACTION	100
4.78-5.46	0.2525	146	0.2188	2760	X-RAY DIFFRACTION	100
5.46-6.85	0.3022	156	0.2486	2708	X-RAY DIFFRACTION	98
6.85-22.85	0.2782	138	0.2326	2879	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	1.8525	-0.1179	-1.1209	4.1158	2.7386	3.8133	-0.6415	0.1948	0.2943	-0.7722	0.1594	-0.1831	0.0108	-0.0664	0.4806	0.8928	0.272	0.1675	0.5205	0.0638	0.6946	-33.6467	-7.1957	-25.4939
2	0.5661	-0.1202	-0.3169	0.3655	-0.0282	1.0427	0.2322	-0.0086	0.2312	0.4316	0.2916	0.1737	-0.688	-0.5231	-0.1479	1.347	0.8652	0.3319	1.2343	0.2462	0.0462	-21.7169	-31.1149	-23.5254
3	0.26	0.3132	-0.2774	9.4475	5.3711	4.0421	0.0445	0.1931	0.2422	0.4524	0.6571	-0.274	-0.3656	0.1735	-0.6488	1.0775	0.5611	0.1873	0.9547	0.089	0.4774	-25.0677	-18.9473	-17.1136
4	7.0303	4.2662	2.8484	5.946	1.6936	3.6183	0.3065	-0.8424	-0.6735	0.3331	-0.2438	0.4185	-0.1877	-0.5007	-0.0728	0.6414	0.3881	0.0382	0.9061	0.1994	0.8862	-39.7365	-24.0054	-25.4151
5	1.1039	-0.4747	0.1294	1.9664	-0.6369	0.5557	0.1614	0.6191	-0.0778	0.5112	-0.0854	0.5732	0.1415	0.133	-0.0709	0.7416	0.3069	0.1365	0.8926	0.191	0.5603	-36.6478	-21.9703	-20.6398
6	4.3766	-0.2714	0.9008	5.5279	0.7394	2.5171	0.1343	0.0061	0.6811	0.4054	-0.4677	0.8995	-0.0578	0.2127	0.357	0.9515	0.3106	0.1552	0.5351	0.0652	0.8443	-28.527	-14.2429	-5.1282
7	0.188	-0.0133	-0.3708	7.9362	2.7461	1.6343	-0.1609	-0.3262	0.0176	0.2563	0.1559	0.9775	-0.1137	0.0309	0.0211	0.4782	0.1563	0.1628	0.6374	0.2222	0.5138	-29.393	-28.5617	-7.094
8	1.071	0.9954	-1.1145	2.2532	-2.1953	2.1764	-0.2301	-0.5749	-0.0673	0.3318	-0.1367	-0.1181	-0.3109	-0.0106	0.325	0.7453	0.181	0.0772	1.189	0.1003	0.454	-22.6218	-35.7373	-4.2466
9	1.6404	-0.0693	0.1605	1.7028	-0.0519	0.8432	0.1863	0.1657	-0.2165	-0.8014	-0.109	0.3023	-0.4478	0.8023	-0.0104	0.4199	-0.2418	0.1096	0.4214	0.0275	0.1358	-1.5554	-4.9454	-58.332
10	1.0163	1.0168	0.8553	2.3219	0.415	1.7071	-0.081	0.2097	0.0373	-0.4178	0.1363	-0.0146	-0.5544	0.7098	-0.0656	0.4037	-0.2044	-0.0095	0.4147	0.0711	0.2199	2.9205	0.6031	-50.828
11	1.5169	-0.0368	0.7813	1.7046	1.4383	4.1705	0.0198	-0.0352	-0.1168	0.0079	0.0913	0.0114	0.1574	0.3393	-0.0959	0.2342	-0.039	0.0232	0.1873	0.0279	0.2018	2.7568	-6.0733	-43.6117
12	2.5679	0.4147	0.6416	1.5423	-0.4207	1.3731	0.0346	0.726	0.1432	-0.1858	-0.0172	-0.1291	-0.1114	0.1459	0.0318	0.3592	0.0312	0.1515	0.4325	0.0987	0.3066	21.9261	-46.412	-81.5774
13	2.8896	0.6733	-1.3969	1.7756	0.8433	4.0572	0.0371	0.5415	0.1572	-0.2466	0.1426	-0.0668	0.0135	-0.3283	-0.107	0.3143	0.0309	-0.0032	0.2914	0.0479	0.1541	0.9069	-60.2704	-73.6247
14	2.6635	1.343	-1.2876	0.7266	-0.8913	1.8478	0.0549	-0.1402	-0.039	0.0339	-0.0072	-0.0622	-0.1526	0.0511	-0.1018	0.2932	0.0703	0.0062	0.203	-0.0248	0.2614	12.4823	-56.0157	-64.1254
15	2.076	0.4255	0.124	1.9284	-0.7342	2.4119	0.0213	0.6359	0.2461	-0.0935	0.4321	0.7274	-0.0328	-0.9148	-0.3583	0.3032	0.0607	0.0463	0.6428	0.1993	0.4679	4.0181	-48.4664	-81.2767
16	2.4935	0.6146	-1.266	1.592	-0.1325	2.7252	0.2079	0.1392	0.4156	0.0954	-0.0012	0.0915	-0.4943	-0.1569	-0.1783	0.3079	0.0629	0.0288	0.2205	0.0514	0.288	8.6939	-44.3027	-66.7026
17	1.3356	-0.8012	-0.599	2.7467	0.1537	1.4863	0.149	0.1889	-0.1193	-0.4051	-0.054	-0.1558	0.119	0.1811	-0.0965	0.3079	-0.0075	-0.0714	0.3428	-0.0203	0.2135	14.6385	-20.9348	-23.3785
18	3.2646	0.4464	-1.5552	6.0389	-0.0215	6.5841	0.6186	-0.4883	0.2484	0.6972	-0.1109	-1.3959	-1.3329	0.796	-0.5149	0.5553	0.0763	-0.0871	0.6976	-0.1504	0.6236	29.7196	-14.3127	-17.9543
19	1.568	-0.318	-0.1082	2.5701	0.4795	1.8465	0.1399	0.0275	-0.2241	-0.0412	0.0517	-0.1779	0.1323	0.195	-0.1667	0.1958	0.0386	-0.0832	0.2645	-0.022	0.2772	20.1984	-26.1721	-15.6647
20	1.2579	0.1549	-1.441	1.6776	0.1895	1.7022	0.0108	-0.1131	-0.136	0.0801	-0.0796	0.1481	-0.2573	-0.3923	0.0366	0.6061	0.4503	0.093	1.3382	0.2124	0.8421	-40.1015	-15.6332	-31.5875

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'D' and (resid 74 through 98 )
2	X-RAY DIFFRACTION	2	chain 'D' and (resid 99 through 208 )
3	X-RAY DIFFRACTION	3	chain 'D' and (resid 209 through 232 )
4	X-RAY DIFFRACTION	4	chain 'D' and (resid 233 through 311 )
5	X-RAY DIFFRACTION	5	chain 'D' and (resid 312 through 343 )
6	X-RAY DIFFRACTION	6	chain 'D' and (resid 344 through 365 )
7	X-RAY DIFFRACTION	7	chain 'D' and (resid 366 through 380 )
8	X-RAY DIFFRACTION	8	chain 'D' and (resid 381 through 407 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 46 through 133 )
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 134 through 271 )
11	X-RAY DIFFRACTION	11	chain 'A' and (resid 272 through 407 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 48 through 98 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 99 through 155 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 156 through 232 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 233 through 270 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 271 through 407 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 46 through 232 )
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 233 through 256 )
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 257 through 407 )
20	X-RAY DIFFRACTION	20	chain 'D' and (resid 45 through 73 )

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