SAXSdb — 5kja

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

Apocarotenoid-15,15'-oxygenase

Synechocystis sp. (strain PCC 6803 / Kazusa)

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	CHLORIDE ION × 1 FE (II) ION × 1 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	CHLORIDE ION × 1 FE (II) ION × 1 water × 1	Consistent with protein count
3	Protein monomer	Monomer	Protein 1	FE (II) ION × 1 water × 1	Consistent with protein count
4	Protein monomer	Monomer	Protein 1	FE (II) ION × 1 water × 1	Consistent with protein count
5	Protein monomer	Monomer	Protein 1	FE (II) ION × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	ACOX_SYNY3
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 Author chain E； 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	5kja
Deposition date deposition_date	2016-06-18
Structure title title	Synechocystis apocarotenoid oxygenase (ACO) mutant - Trp149Ala
Keywords keywords	iron-coordination, active site, carotenoid binding, ligand interaction, non-heme iron, mutagenesis, OXIDOREDUCTASE; 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.

5kja__assembly_1__model_1

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

Download this curve (.dat)

5kja__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5kja__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	22.82 Å
Rg (electron density)	21.65 Å
Total Rg	22.61 Å
Atom count	3780
Residues	482
Excluded volume	66992 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5kja__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`5kja__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`5kja__assembly_3__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`5kja__assembly_4__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
5	1	`5kja__assembly_5__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-15,15'-oxygenase
Molecular weight formula_weight	54229.1 kDa
EC 编号 ec_number	1.13.11.75
Mutation mutation	W149A
Source method src_method	man
Copy count entity_count	5

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E
Atom count atom_count	18975

MVTSPPTSSPSQRSYSPQDWLRGYQSQPQEWDYWVEDVEGSIPPDLQGTLYRNGPGLLEIGDRPLKHPFDGDGMVTAFKFPGDGRVHFQSKFVRTQGYVEEQKAGKMIYRGVFGSQPAGGWLKTIFDLRLKNIANTNITYWGDRLLALAEGGQPHRLEPSNLATIGLDDLGGILAEGQPLSAHPRIDPASTFDGGQPCYVTFSIKSSLSSTLTLLELDPQGKLLRQKTETFPGFAFIHDFAITPHYAIFLQNNVTLNGLPYLFGLRGAGECVQFHPDKPAQIILVPRDGGEIKRIPVQAGFVFHHANAFEENGKIILDSICYNSLPQVDTDGDFRSTNFDNLDPGQLWRFTIDPAAATVEKQLMVSRCCEFPVVHPQQVGRPYRYVYMGAAHHSTGNAPLQAILKVDLESGTETLRSFAPHGFAGEPIFVPRPGGVAEDDGWLLCLIYKADLHRSELVILDAQDITAPAIATLKLKHHIPYPLHGSWAQT

Source Source

Source organism organism	Synechocystis sp. (strain PCC 6803 / Kazusa)
NCBI taxonomy ID ncbi_taxonomy_id	1111708
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	nat
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	FE (II) ION
Molecular weight formula_weight	55.8 kDa
Source method src_method	man
Copy count entity_count	5

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	154

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6. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (5 domains)

Domain ID domain_id	d5kjaa_
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	d5kjab_
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	d5kjac_
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	d5kjad_
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	d5kjae_
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	118.140 Å
Unit-cell length b length_b	125.260 Å
Unit-cell length c length_c	203.570 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	20

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

Resolution resolution	2.800 Å
Low-resolution limit resolution_low	48.620 Å
R factor r_factor	0.2000
R_work r_work	0.1980
R_free r_free	0.2391

Synechocystis apocarotenoid oxygenase (ACO) mutant - Trp149Ala

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

Apocarotenoid-15,15'-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

5kja__assembly_1__model_1

5kja__assembly_1__model_1 | I(q)

5kja__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

6. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (5 domains)

7. Citations (1)

Synechocystis apocarotenoid oxygenase (ACO) mutant - Trp149Ala

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

Apocarotenoid-15,15'-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

5kja__assembly_1__model_1

5kja__assembly_1__model_1 | I(q)

5kja__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

6. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (5 domains)

7. Citations (1)