PDB-8qn1: OPR3 variant - R283D

ID or keywords:

Entry

Database: PDB / ID: 8qn1

Title

OPR3 variant - R283D

Components

12-oxophytodienoate reductase 3

Keywords

FLAVOPROTEIN / Old Yellow Enzyme / ene-reductase / flavoenzyme / oxidoreductase

Function / homology

Function and homology information

12-oxophytodienoate reductase / 12-oxophytodienoate reductase activity / jasmonic acid biosynthetic process / oxylipin biosynthetic process / peroxisome / FMN binding / identical protein binding
Similarity search - Function

Biological species

Solanum lycopersicum (tomato)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.75 Å

Authors

Bijelic, A. / Macheroux, P. / Kerschbaumer, B.

Funding support

Austria, 1items

Citation

Journal: Sci Rep / Year: 2024
Title: Analysis of homodimer formation in 12-oxophytodienoate reductase 3 in solutio and crystallo challenges the physiological role of the dimer.
Authors: Kerschbaumer, B. / Macheroux, P. / Bijelic, A.

History

Deposition	Sep 25, 2023	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Aug 14, 2024	Provider: repository / Type: Initial release
Revision 1.1	Aug 21, 2024	Group: Database references / Category: citation / citation_author Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8qn1.cif.gz	598.7 KB	Display	PDBx/mmCIF format
PDB format	pdb8qn1.ent.gz	491.9 KB	Display	PDB format
PDBx/mmJSON format	8qn1.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/qn/8qn1 ftp://data.pdbj.org/pub/pdb/validation_reports/qn/8qn1	HTTPS FTP

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Related structure data

Related structure data	8qn9C 8s8vC 8s8yC 9em0C 9em2C 9em3C 9em4C 9em5C 9em6C 8qmx 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

Deposited unit

A: 12-oxophytodienoate reductase 3

C: 12-oxophytodienoate reductase 3

B: 12-oxophytodienoate reductase 3

D: 12-oxophytodienoate reductase 3

hetero molecules

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

1

A: 12-oxophytodienoate reductase 3

B: 12-oxophytodienoate reductase 3

hetero molecules

defined by author
Evidence: gel filtration
84 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: 12-oxophytodienoate reductase 3

D: 12-oxophytodienoate reductase 3

hetero molecules

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

Unit cell

Length a, b, c (Å)	81.070, 90.780, 111.740
Angle α, β, γ (deg.)	90.00, 109.64, 90.00
Int Tables number	4
Space group name H-M	P12₁1
Symmetry operation	#1: x,y,z #2: -x,y+1/2,-z

#1: Protein	12-oxophytodienoate reductase 3 Mass: 41486.070 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Solanum lycopersicum (tomato) / Gene: OPR3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9FEW9
#2: Chemical	ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE Mass: 456.344 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₁₇H₂₁N₄O₉P
#3: Chemical	ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₆H₁₄O₂ / Comment: precipitant*YM
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1109 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	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: 2.18 Å³/Da / Density % sol: 43.64 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 100 mM Tris-HCl, 50 mM sodium tartate, 8% PEG8000

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.0332 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 19, 2022
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.0332 Å / Relative weight: 1
Reflection	Resolution: 1.75→46.28 Å / Num. obs: 296522 / % possible obs: 97.94 % / Redundancy: 6.9 % / B_iso Wilson estimate: 24.87 Å² / CC_1/2: 0.996 / Net I/σ(I): 9.3
Reflection shell	Resolution: 1.75→1.77 Å / Num. unique obs: 4973 / CC_1/2: 0.725

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Processing

Software

Name	Version	Classification
PHENIX	(dev_4761: ???)	refinement
XDS		data reduction
XSCALE		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.75→46.28 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.92 / Phase error: 31.04 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2542	14823	5 %
R_work	0.2349	-	-
obs	0.2359	296522	97.97 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 1.75→46.28 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	11564	0	16	1109	12689

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	11863
X-RAY DIFFRACTION	f_angle_d	0.775	16162
X-RAY DIFFRACTION	f_dihedral_angle_d	13.732	4248
X-RAY DIFFRACTION	f_chiral_restr	0.046	1782
X-RAY DIFFRACTION	f_plane_restr	0.006	2095

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 (%)
1.75-1.77	0.3355	488	0.3364	9225	X-RAY DIFFRACTION	96
1.77-1.79	0.3312	481	0.3207	9263	X-RAY DIFFRACTION	97
1.79-1.81	0.3361	488	0.3146	9285	X-RAY DIFFRACTION	97
1.81-1.84	0.3425	495	0.3085	9347	X-RAY DIFFRACTION	98
1.84-1.86	0.3352	495	0.3073	9316	X-RAY DIFFRACTION	97
1.86-1.89	0.2827	497	0.2968	9491	X-RAY DIFFRACTION	98
1.89-1.91	0.3099	494	0.2922	9307	X-RAY DIFFRACTION	98
1.91-1.94	0.2886	493	0.2881	9455	X-RAY DIFFRACTION	98
1.94-1.97	0.2887	499	0.2824	9456	X-RAY DIFFRACTION	98
1.97-2	0.2997	501	0.2779	9422	X-RAY DIFFRACTION	99
2-2.04	0.2847	497	0.2664	9425	X-RAY DIFFRACTION	98
2.04-2.07	0.2802	495	0.2651	9475	X-RAY DIFFRACTION	98
2.07-2.11	0.3102	492	0.2549	9375	X-RAY DIFFRACTION	98
2.11-2.16	0.2543	468	0.2516	8874	X-RAY DIFFRACTION	93
2.16-2.2	0.2728	499	0.2491	9494	X-RAY DIFFRACTION	98
2.2-2.26	0.2669	501	0.244	9474	X-RAY DIFFRACTION	99
2.26-2.31	0.2845	497	0.2478	9464	X-RAY DIFFRACTION	99
2.31-2.38	0.2958	496	0.2503	9465	X-RAY DIFFRACTION	99
2.38-2.44	0.2876	503	0.2524	9484	X-RAY DIFFRACTION	99
2.44-2.52	0.2939	498	0.2463	9500	X-RAY DIFFRACTION	99
2.52-2.61	0.2828	493	0.2533	9521	X-RAY DIFFRACTION	99
2.61-2.72	0.2741	495	0.2388	9439	X-RAY DIFFRACTION	99
2.72-2.84	0.2634	492	0.2441	9450	X-RAY DIFFRACTION	99
2.84-2.99	0.2504	494	0.2347	9358	X-RAY DIFFRACTION	98
2.99-3.18	0.2369	477	0.2296	8997	X-RAY DIFFRACTION	94
3.18-3.43	0.2264	499	0.2174	9525	X-RAY DIFFRACTION	99
3.43-3.77	0.239	505	0.2055	9565	X-RAY DIFFRACTION	100
3.77-4.31	0.2206	507	0.2009	9557	X-RAY DIFFRACTION	99
4.31-5.43	0.2195	494	0.1994	9465	X-RAY DIFFRACTION	99
5.43-46.28	0.1967	490	0.2062	9225	X-RAY DIFFRACTION	96

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	1.2888	0.0888	-0.1251	2.4937	0.6494	1.9403	-0.0108	-0.1543	-0.0215	0.1513	0.1178	0.0102	0.0471	0.0223	0.006	0.2461	0.0194	-0.0168	0.2648	0.0057	0.1526	34.104	-4.174	12.801
2	0.8277	-0.4867	-0.1812	1.5564	0.5692	1.5868	-0.0204	0.039	-0.1549	0.0091	-0.0018	0.1563	0.2694	-0.1215	0.0476	0.3356	-0.0246	-0.005	0.286	-0.0081	0.2158	31.808	-11.989	3.206
3	0.8938	0.7139	0.3736	4.1497	-0.3846	1.8757	0.04	0.1271	-0.2348	-0.3836	-0.1134	-0.7897	0.0893	0.3279	-0.1123	0.3845	0.0035	0.0656	0.3603	0.0026	0.2027	46.934	-9.43	-11.991
4	2.4997	0.1476	-0.2946	1.7871	0.2619	1.4859	-0.0877	0.1547	-0.0829	-0.3135	0.0414	0.2048	-0.0517	-0.0471	0.0763	0.3497	0.0049	-0.0096	0.2527	-0.0147	0.1727	33.493	-5.003	-7.517
5	2.5847	0.2259	0.1946	1.7656	-0.2527	2.0754	-0.0589	0.3138	0.5168	-0.2259	-0.0433	0.1719	-0.3928	-0.0647	0.0506	0.4061	-0.046	-0.0675	0.2103	0.0523	0.2132	34.82	6.663	-12.104
6	1.6886	0.0041	0.751	2.3336	0.2023	0.9589	0.0477	0.0545	0.2782	-0.0935	-0.046	-0.2377	-0.1362	0.1836	-0.0095	0.3765	-0.0283	0.015	0.3002	0.0169	0.2712	41.748	8.178	-0.723
7	1.1302	-0.0169	0.466	1.6693	-0.1175	1.4308	-0.0007	0.0365	0.1633	-0.0239	-0.0495	-0.336	-0.1982	0.0214	0.0057	0.369	-0.0346	-0.0212	0.2916	-0.0272	0.275	44.247	10.302	10.767
8	0.5075	-0.476	0.154	1.8653	0.4299	1.7038	-0.1326	-0.1547	0.1502	0.6963	0.1734	-0.4861	0.1882	0.1675	-0.052	0.4227	-0.017	-0.0694	0.3644	-0.0102	0.245	44.201	-4.213	18.969
9	1.7643	0.4261	-0.0634	2.5987	0.1916	1.5128	-0.2028	0.1716	-0.202	0.0933	0.1921	-0.131	0.3169	-0.039	-0.0023	0.4411	0.0234	-0.0256	0.3241	0.0014	0.2253	43.557	-18.453	12.453
10	0.5511	0.0802	0.1287	2.2996	0.8301	2.4824	-0.0366	0.0494	-0.0992	0.1011	-0.0366	0.2787	-0.068	-0.0714	0.0768	0.144	-0.0107	0.0361	0.09	0.0131	0.1983	55.519	-1.757	65.002
11	0.8094	-0.0992	-0.1932	2.144	0.0533	0.5954	0.033	-0.0291	-0.1021	-0.1565	-0.0558	0.2961	0.0084	-0.0053	0.0049	0.1161	-0.0054	-0.0276	0.1119	-0.023	0.1996	56.327	-0.847	45.846
12	1.1174	0.0602	0.2614	1.6983	0.4357	0.5575	-0.0814	-0.0247	-0.0913	0.0041	0.0437	0.0642	-0.0118	0.0527	0.03	0.143	-0.0168	-0.0054	0.1155	0.0207	0.2028	59.716	13.539	50.077
13	0.5111	0.1225	-0.5169	0.1297	0.0502	0.9772	0.0841	0.0984	0.2146	0.1357	-0.1665	-0.4743	-0.4022	0.4549	-0.2232	0.1422	-0.06	0.0383	0.2673	0.0387	0.421	68.156	12.402	54.444
14	1.0521	0.2833	0.2	2.5714	-0.5668	0.8684	0.046	0.0164	0.2203	0.267	-0.039	-0.1782	-0.0128	0.1476	-0.0199	0.1907	-0.0078	-0.0008	0.1662	-0.025	0.1871	66.249	15.246	62.904
15	1.026	0.0317	0.2876	2.5256	0.3949	1.7477	-0.0149	-0.0653	-0.1268	0.4706	-0.0204	-0.1648	0.2122	0.0805	0.0288	0.2184	0.0137	-0.0219	0.1502	0.0024	0.1475	66.026	-4.663	68.729
16	0.9477	0.1662	-0.1787	2.765	-0.4334	1.8213	-0.1129	-0.2098	-0.0117	-0.0805	0.1451	-0.0135	0.41	0.234	0.0325	0.3095	0.0996	0.0076	0.4032	-0.0083	0.2051	81.009	2.953	9.02
17	1.1858	-0.6666	-0.0765	2.1681	0.3158	1.5712	0.0577	-0.1042	0.2604	0.1929	-0.0556	-0.274	-0.2523	-0.0432	-0.015	0.3294	-0.0268	-0.0172	0.3917	-0.0084	0.2777	84.857	12.531	4.313
18	2.5947	-0.0404	1.3784	1.5564	-0.33	2.3378	-0.0164	0.3332	0.1334	-0.2199	-0.0712	-0.0863	-0.2848	-0.0551	0.077	0.3512	0.0289	0.0316	0.3389	0.0139	0.2512	78.401	9.181	-10.877
19	2.8811	0.231	0.8013	1.6443	-0.1495	2.2371	0.1279	0.812	-0.3843	-0.4962	0.0172	-0.114	-0.1193	0.0146	-0.1633	0.4606	0.0365	0.032	0.482	-0.0522	0.339	80.831	-3.71	-17.223
20	1.3094	0.352	-1.0172	2.7186	0.1614	2.1701	-0.0478	0.3063	-0.188	-0.158	-0.0618	0.0708	0.2085	-0.1258	0.0651	0.3422	-0.0574	-0.0092	0.356	-0.0209	0.3002	77.889	-7.39	-8.126
21	2.9922	1.3008	-0.3728	0.4919	-0.1536	-0.0842	0.3701	-0.3691	-0.0912	0.1802	-0.206	0.0918	-0.1005	-0.1017	-0.2086	0.404	-0.0254	0.009	0.4182	-0.0502	0.3469	67.502	-8.83	0.495
22	1.5246	0.0362	-1.1103	0.9347	0.3625	1.3631	0.0389	-0.0792	-0.1351	0.342	-0.2269	0.3268	0.0672	-0.2376	0.1462	0.3232	0.0109	0.0036	0.4029	0.0014	0.24	71.405	3.119	11.855
23	1.5325	-0.5543	-0.6074	2.7581	-0.6141	1.5371	-0.0233	-0.173	-0.0411	0.3132	-0.1012	-0.3131	-0.0331	-0.0212	0.1494	0.1645	-0.0501	-0.0431	0.1932	0.0298	0.2737	102.743	10.524	61.736
24	2.3751	-0.3226	-0.0328	1.8525	0.029	1.3132	0.0989	0.2964	-0.1002	-0.367	-0.0581	-0.1315	-0.0739	-0.2178	-0.0358	0.189	0.0385	0.0292	0.2317	0.0214	0.29	102.57	12.7	42.759
25	0.8879	-0.1936	-0.3211	2.6089	-0.577	1.4551	-0.1108	0.0274	-0.191	-0.3126	0.013	-0.0516	-0.0534	-0.1691	0.1418	0.2355	0.0101	0.0022	0.2673	-0.0506	0.4749	99.633	-2.233	44.306
26	1.3919	0.31	0.1753	0.233	-0.1224	0.035	-0.0959	0.0644	-0.4199	-0.061	0.0343	-0.0345	0.0408	0.0264	0.0499	0.2243	-0.0219	0.0316	0.3104	-0.0332	0.4531	86.619	-2.007	53.135
27	1.7117	0.3252	-0.0511	2.1142	0.2522	0.8157	0.0698	-0.2079	-0.1935	0.3568	-0.1671	0.2355	0.0212	-0.1141	0.1142	0.2471	-0.0433	0.0316	0.2737	0.0354	0.3324	92.838	5.62	62.673

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	( CHAIN A AND RESID 10:43 )	A	10 - 43
2	X-RAY DIFFRACTION	2	( CHAIN A AND RESID 44:122 )	A	44 - 122
3	X-RAY DIFFRACTION	3	( CHAIN A AND RESID 123:142 )	A	123 - 142
4	X-RAY DIFFRACTION	4	( CHAIN A AND RESID 143:196 )	A	143 - 196
5	X-RAY DIFFRACTION	5	( CHAIN A AND RESID 197:229 )	A	197 - 229
6	X-RAY DIFFRACTION	6	( CHAIN A AND RESID 230:297 )	A	230 - 297
7	X-RAY DIFFRACTION	7	( CHAIN A AND RESID 298:332 )	A	298 - 332
8	X-RAY DIFFRACTION	8	( CHAIN A AND RESID 333:365 )	A	333 - 365
9	X-RAY DIFFRACTION	9	( CHAIN A AND RESID 366:384 )	A	366 - 384
10	X-RAY DIFFRACTION	10	( CHAIN B AND RESID 10:66 )	B	10 - 66
11	X-RAY DIFFRACTION	11	( CHAIN B AND RESID 67:229 )	B	67 - 229
12	X-RAY DIFFRACTION	12	( CHAIN B AND RESID 230:270 )	B	230 - 270
13	X-RAY DIFFRACTION	13	( CHAIN B AND RESID 271:296 )	B	271 - 296
14	X-RAY DIFFRACTION	14	( CHAIN B AND RESID 302:332 )	B	302 - 332
15	X-RAY DIFFRACTION	15	( CHAIN B AND RESID 333:384 )	B	333 - 384
16	X-RAY DIFFRACTION	16	( CHAIN C AND RESID 10:43 )	C	10 - 43
17	X-RAY DIFFRACTION	17	( CHAIN C AND RESID 44:99 )	C	44 - 99
18	X-RAY DIFFRACTION	18	( CHAIN C AND RESID 100:196 )	C	100 - 196
19	X-RAY DIFFRACTION	19	( CHAIN C AND RESID 197:229 )	C	197 - 229
20	X-RAY DIFFRACTION	20	( CHAIN C AND RESID 230:270 )	C	230 - 270
21	X-RAY DIFFRACTION	21	( CHAIN C AND RESID 271:311 )	C	271 - 311
22	X-RAY DIFFRACTION	22	( CHAIN C AND RESID 312:384 )	C	312 - 384
23	X-RAY DIFFRACTION	23	( CHAIN D AND RESID 10:66 )	D	10 - 66
24	X-RAY DIFFRACTION	24	( CHAIN D AND RESID 67:229 )	D	67 - 229
25	X-RAY DIFFRACTION	25	( CHAIN D AND RESID 230:270 )	D	230 - 270
26	X-RAY DIFFRACTION	26	( CHAIN D AND RESID 271:299 )	D	271 - 299
27	X-RAY DIFFRACTION	27	( CHAIN D AND RESID 300:384 )	D	300 - 384

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Movie

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Structure viewers

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Open data

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Validation report

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Assembly

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Experimental details

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Experiment

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Sample preparation

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Data collection

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About Yorodumi

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

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

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Yorodumi