SAXSdb — 2biw

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

APOCAROTENOID-CLEAVING OXYGENASE

SYNECHOCYSTIS SP.

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	(3R)-3-HYDROXY-8'-APOCAROTENOL × 1 FE (III) ION × 1 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	(3R)-3-HYDROXY-8'-APOCAROTENOL × 1 FE (III) ION × 1 water × 1	Consistent with protein count
3	Protein monomer	Monomer	Protein 1	(3R)-3-HYDROXY-8'-APOCAROTENOL × 1 FE (III) ION × 1 water × 1	Consistent with protein count
4	Protein monomer	Monomer	Protein 1	(3R)-3-HYDROXY-8'-APOCAROTENOL × 1 FE (III) ION × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	P74334
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–490； UniProt 1–490 Author chain B； PDBConstruct 1–490； UniProt 1–490 Author chain C； PDBConstruct 1–490； UniProt 1–490 Author chain D； PDBConstruct 1–490； UniProt 1–490

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	2biw
Deposition date deposition_date	2005-01-26
Structure title title	Crystal structure of apocarotenoid cleavage oxygenase from Synechocystis, native enzyme
Keywords keywords	OXYGENASE, NON-HEME IRON, CAROTENOID CLEAVAGE, RETINAL FORMATION, OXIDOREDUCTASE, DIOXYGENASE; OXIDOREDUCTASE
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.

2biw__assembly_4__model_1

Assembly 4 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

2biw__assembly_4__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2biw__assembly_4__model_1 | P(r) · Pending

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

Rg（Guinier）	22.60 Å
Rg (electron density)	21.36 Å
Total Rg	22.35 Å
Atom count	3800
Residues	479
Excluded volume	67529 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2biw__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2biw__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`2biw__assembly_3__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`2biw__assembly_4__model_1`	monomeric （1）	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	APOCAROTENOID-CLEAVING OXYGENASE
Molecular weight formula_weight	54344.2 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	15742

MVTSPPTSSPSQRSYSPQDWLRGYQSQPQEWDYWVEDVEGSIPPDLQGTLYRNGPGLLEIGDRPLKHPFDGDGMVTAFKFPGDGRVHFQSKFVRTQGYVEEQKAGKMIYRGVFGSQPAGGWLKTIFDLRLKNIANTNITYWGDRLLALWEGGQPHRLEPSNLATIGLDDLGGILAEGQPLSAHPRIDPASTFDGGQPCYVTFSIKSSLSSTLTLLELDPQGKLLRQKTETFPGFAFIHDFAITPHYAIFLQNNVTLNGLPYLFGLRGAGECVQFHPDKPAQIILVPRDGGEIKRIPVQAGFVFHHANAFEENGKIILDSICYNSLPQVDTDGDFRSTNFDNLDPGQLWRFTIDPAAATVEKQLMVSRCCEFPVVHPQQVGRPYRYVYMGAAHHSTGNAPLQAILKVDLESGTETLRSFAPHGFAGEPIFVPRPGGVAEDDGWLLCLIYKADLHRSELVILDAQDITAPAIATLKLKHHIPYPLHGSWAQT

Source Source

Source organism organism	SYNECHOCYSTIS SP.
NCBI taxonomy ID ncbi_taxonomy_id	1148
Host organism host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 non-polymer

Description description	(3R)-3-HYDROXY-8'-APOCAROTENOL
Molecular weight formula_weight	434.7 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 non-polymer

Description description	FE (III) ION
Molecular weight formula_weight	55.8 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	542

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6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d2biwa_
Class class	b — All beta proteins
Fold Fold fold	b.69 — 7-bladed beta-propeller
Superfamily Superfamily superfamily	b.69.15 — Retinal pigment epithelial membrane protein-like
Family Family family	b.69.15.1 — RPE65-like

Domain ID domain_id	d2biwb_
Class class	b — All beta proteins
Fold Fold fold	b.69 — 7-bladed beta-propeller
Superfamily Superfamily superfamily	b.69.15 — Retinal pigment epithelial membrane protein-like
Family Family family	b.69.15.1 — RPE65-like

Domain ID domain_id	d2biwc_
Class class	b — All beta proteins
Fold Fold fold	b.69 — 7-bladed beta-propeller
Superfamily Superfamily superfamily	b.69.15 — Retinal pigment epithelial membrane protein-like
Family Family family	b.69.15.1 — RPE65-like

Domain ID domain_id	d2biwd_
Class class	b — All beta proteins
Fold Fold fold	b.69 — 7-bladed beta-propeller
Superfamily Superfamily superfamily	b.69.15 — Retinal pigment epithelial membrane protein-like
Family Family family	b.69.15.1 — RPE65-like

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Unit-cell length a length_a	119.046 Å
Unit-cell length b length_b	125.278 Å
Unit-cell length c length_c	203.086 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	16

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.390 Å
Low-resolution limit resolution_low	44.410 Å
R factor r_factor	0.1820
R_work r_work	0.1800
R_free r_free	0.2240

Crystal structure of apocarotenoid cleavage oxygenase from Synechocystis, native enzyme

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

APOCAROTENOID-CLEAVING OXYGENASE

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

2biw__assembly_4__model_1

2biw__assembly_4__model_1 | I(q)

2biw__assembly_4__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

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (4 domains)

7. Citations (1)

Crystal structure of apocarotenoid cleavage oxygenase from Synechocystis, native enzyme

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

APOCAROTENOID-CLEAVING OXYGENASE

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

2biw__assembly_4__model_1

2biw__assembly_4__model_1 | I(q)

2biw__assembly_4__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

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (4 domains)

7. Citations (1)