PDB-8s8v: OPR3 variant R283D in its monomeric form

ID or keywords:

Entry

Database: PDB / ID: 8s8v

Title

OPR3 variant R283D in its monomeric form

Components

12-oxophytodienoate reductase 3

Keywords

FLAVOPROTEIN / ene-reductase / Old Yellow Enzyme

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: 3 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	Mar 7, 2024	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 Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8s8v.cif.gz	282.7 KB	Display	PDBx/mmCIF format
PDB format	pdb8s8v.ent.gz	228 KB	Display	PDB format
PDBx/mmJSON format	8s8v.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8s8v_validation.pdf.gz	1 MB	Display	wwPDB validaton report
Full document	8s8v_full_validation.pdf.gz	1 MB	Display
Data in XML	8s8v_validation.xml.gz	27.4 KB	Display
Data in CIF	8s8v_validation.cif.gz	36.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/s8/8s8v ftp://data.pdbj.org/pub/pdb/validation_reports/s8/8s8v	HTTPS FTP

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Related structure data

Related structure data	8qn1C 8qn9C 8s8yC 9em0C 9em2C 9em3C 9em4C 9em5C 9em6C 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

B: 12-oxophytodienoate reductase 3

hetero molecules

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

1

A: 12-oxophytodienoate reductase 3

hetero molecules

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

2

B: 12-oxophytodienoate reductase 3

hetero molecules

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

Unit cell

Length a, b, c (Å)	86.390, 89.314, 95.528
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	12-oxophytodienoate reductase 3 Mass: 44359.094 Da / Num. of mol.: 2 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.: 2 / Source method: obtained synthetically / Formula: C₁₇H₂₁N₄O₉P
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: 2.08 Å³/Da / Density % sol: 40.78 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.1 M MES/Tris (6.5), 10 mM ammonium sulfate, 8-16% PEG8000

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.87 Å
Detector	Type: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Feb 8, 2024
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.87 Å / Relative weight: 1
Reflection	Resolution: 2.69→44.66 Å / Num. obs: 133610 / % possible obs: 94.4 % / Redundancy: 3.6 % / CC_1/2: 0.9 / R_pim(I) all: 0.29 / Net I/σ(I): 1.71
Reflection shell	Resolution: 2.69→2.76 Å / Num. unique obs: 37427 / CC_1/2: 0.18 / R_pim(I) all: 0.89

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Processing

Software

Name	Version	Classification
PHENIX	(1.21_5207: ???)	refinement
XDS		data reduction
XSCALE		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 3→44.66 Å / SU ML: 0.45 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 30.49 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2966	1445	10.03 %
R_work	0.2497	-	-
obs	0.2545	14404	93.95 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 3→44.66 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5451	0	62	0	5513

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.005	5647
X-RAY DIFFRACTION	f_angle_d	1.034	7706
X-RAY DIFFRACTION	f_dihedral_angle_d	14.385	1996
X-RAY DIFFRACTION	f_chiral_restr	0.061	858
X-RAY DIFFRACTION	f_plane_restr	0.012	999

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 (%)
3-3.11	0.3386	136	0.2997	1226	X-RAY DIFFRACTION	91
3.11-3.23	0.3316	134	0.2881	1284	X-RAY DIFFRACTION	94
3.23-3.38	0.301	150	0.2803	1301	X-RAY DIFFRACTION	96
3.38-3.56	0.3213	149	0.2561	1307	X-RAY DIFFRACTION	96
3.56-3.78	0.3449	142	0.249	1283	X-RAY DIFFRACTION	95
3.78-4.07	0.2666	149	0.2324	1304	X-RAY DIFFRACTION	95
4.07-4.48	0.275	148	0.2297	1298	X-RAY DIFFRACTION	94
4.48-5.13	0.2549	143	0.2282	1309	X-RAY DIFFRACTION	94
5.13-6.46	0.3301	140	0.2553	1301	X-RAY DIFFRACTION	92
6.46-44.66	0.2762	154	0.2391	1346	X-RAY DIFFRACTION	91

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	0.1651	-0.0831	-0.0206	0.4887	-0.3647	0.4243	0.0357	-0.2546	-0.1112	0.2372	-0.0706	0.0052	0.078	0.0206	0.0913	0.32	0.0046	0.0182	0.2831	0.029	0.3279	3.3783	17.7399	14.7122
2	0.9753	-0.5079	0.8595	1.0287	-0.6151	0.7922	-0.0269	0.0797	0.1355	0.1522	-0.0255	0.0458	-0.1003	0.0767	-0.0981	0.3226	-0.0448	0.0739	0.219	-0.0391	0.3205	7.7379	28.6074	28.0175
3	0.4441	-0.2206	-0.3337	0.9126	0.163	0.6898	0.0535	0.1254	-0.2403	0.0822	-0.2785	0.0935	0.0271	0.1389	-0.0897	0.2741	-0.0339	-0.0293	0.3955	0.0969	0.324	-8.5395	26.5865	12.9854
4	0.0938	-0.0876	0.2984	0.0767	-0.2239	1.241	-0.0253	0.0829	0.13	-0.1134	-0.0107	0.1945	0.2101	0.227	0.1324	0.3232	-0.0674	0.0441	0.1975	0.0595	0.3521	46.4599	28.6456	33.8855
5	1.1012	-0.3325	0.6941	1.1677	0.0317	1.9008	0.1762	0.139	0.0845	-0.1623	-0.1768	-0.3789	-0.192	0.4008	-0.1673	0.2476	-0.0421	0.0398	0.1701	-0.0263	0.3174	51.8142	27.2012	16.4951
6	0.5112	0.3634	-0.115	2.1182	0.2181	0.2457	0.0601	0.0536	-0.4428	-0.6076	0.1508	-0.1961	-0.2573	0.1722	0.2353	0.3764	0.0676	-0.042	0.273	-0.0045	0.2988	52.9774	15.726	20.5914
7	1.2854	-0.4297	1.0458	0.8098	-0.0303	2.0421	0.1495	0.2888	0.0724	0.0255	-0.0369	-0.1154	0.1379	0.2063	0.1138	0.358	-0.0505	-0.019	0.1351	0.0004	0.3024	45.1836	9.656	26.1903
8	1.4403	-0.0361	-0.4059	1.1609	0.1981	0.8988	0.2057	0.2704	0.1376	-0.1178	-0.3176	0.1711	0.1625	-0.3574	-0.0658	0.3741	-0.0728	-0.045	0.2833	0.0252	0.2752	32.4241	23.7216	36.389

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 10 through 122 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 123 through 270 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 271 through 384 )
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 10 through 122 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 123 through 176 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 177 through 229 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 230 through 311 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 312 through 384 )

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