SAXSdb — 8qn1

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1. Protein Identity and Related Structures Protein Identity & Related Structures

12-oxophytodienoate reductase 3

Solanum lycopersicum

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	FLAVIN MONONUCLEOTIDE × 2 (4S)-2-METHYL-2,4-PENTANEDIOL × 1 water × 2	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	FLAVIN MONONUCLEOTIDE × 2 (4S)-2-METHYL-2,4-PENTANEDIOL × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	OPR3_SOLLC
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–375； UniProt 10–384 Author chain B； PDBConstruct 1–375； UniProt 10–384 Author chain C； PDBConstruct 1–375； UniProt 10–384 Author chain D； PDBConstruct 1–375； UniProt 10–384

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	8qn1
Deposition date deposition_date	2023-09-25
Structure title title	OPR3 variant - R283D
Keywords keywords	Old Yellow Enzyme, ene-reductase, flavoenzyme, oxidoreductase, FLAVOPROTEIN; FLAVOPROTEIN
Experimental Method method	X-RAY DIFFRACTION

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

8qn1__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

8qn1__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

8qn1__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	28.36 Å
Rg (electron density)	27.66 Å
Total Rg	28.43 Å
Atom count	5826
Residues	745
Excluded volume	102330 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`8qn1__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`8qn1__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	12-oxophytodienoate reductase 3
Molecular weight formula_weight	41486.1 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C,B,D
Atom count atom_count	12802

NPLFSPYKMGKFNLSHRVVLAPMTRCRALNNIPQAALGEYYEQRATAGGFLITEGTMISPTSAGFPHVPGIFTKEQVREWKKIVDVVHAKGAVIFCQLWHVGRASHEVYQPAGAAPISSTEKPISNRWRILMPDGTHGIYPKPRAIGTYEISQVVEDYRRSALNAIEAGFDGIEIHGAHGYLIDQFLKDGINDRTDEYGGSLANRCKFITQVVQAVVSAIGADRVGVRVSPAIDHLDAMDSNPLSLGLAVVERLNKIQLHSGSKLAYLHVTQPDYVAYGQTEAGRLGSEEEEARLMRTLRNAYQGTFICSGGYTRELGIEAVAQGDADLVSYGRLFISNPDLVMRIKLNAPLNKYNRKTFYTQDPVVGYTDYPFL

Source Source

Source organism organism	Solanum lycopersicum
Common name common_name	tomato
NCBI taxonomy ID ncbi_taxonomy_id	4081
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	FLAVIN MONONUCLEOTIDE
Molecular weight formula_weight	456.3 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 non-polymer

Description description	(4S)-2-METHYL-2,4-PENTANEDIOL
Molecular weight formula_weight	118.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1109

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Unit-cell length a length_a	81.070 Å
Unit-cell length b length_b	90.780 Å
Unit-cell length c length_c	111.740 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	109.64 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	monoclinic

Resolution resolution	1.750 Å
Low-resolution limit resolution_low	46.280 Å
R factor r_factor	0.2359
R_work r_work	0.2349
R_free r_free	0.2542

OPR3 variant - R283D

1. Protein Identity and Related Structures Protein Identity & Related Structures

12-oxophytodienoate reductase 3

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

8qn1__assembly_1__model_1

8qn1__assembly_1__model_1 | I(q)

8qn1__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

7. Citations (1)

OPR3 variant - R283D

1. Protein Identity and Related Structures Protein Identity & Related Structures

12-oxophytodienoate reductase 3

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

8qn1__assembly_1__model_1

8qn1__assembly_1__model_1 | I(q)

8qn1__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

7. Citations (1)