5tuw

Crystal structure of Orange Carotenoid Protein with partial loss of 3'OH Echinenone chromophore

Method: X-RAY DIFFRACTION

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

Orange carotenoid-binding protein

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 homooligomer	Homooligomer	Protein 6	GLYCEROL × 4 (3'R)-3'-hydroxy-beta,beta-caroten-4-one × 6 water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	OCP_SYNY3
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–317； UniProt 1–317 Author chain B； PDBConstruct 1–317； UniProt 1–317 Author chain C； PDBConstruct 1–317； UniProt 1–317 Author chain D； PDBConstruct 1–317； UniProt 1–317 Author chain E； PDBConstruct 1–317； UniProt 1–317 Author chain F； PDBConstruct 1–317； UniProt 1–317

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	5tuw
Deposition date deposition_date	2016-11-07
Structure title title	Crystal structure of Orange Carotenoid Protein with partial loss of 3'OH Echinenone chromophore
Keywords keywords	Photoreceptor, Photoprotection, Dynamic crystallography, Carotenoid binding protein; Carotenoid binding protein
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.

5tuw__assembly_1__model_1

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

Download this curve (.dat)

5tuw__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5tuw__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	42.05 Å
Rg (electron density)	41.60 Å
Total Rg	41.90 Å
Atom count	14715
Residues	1830
Excluded volume	258250 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5tuw__assembly_1__model_1`	hexameric （6）	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	Orange carotenoid-binding protein
Molecular weight formula_weight	35513.5 kDa
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F
Atom count atom_count	15054

MPFTIDSARGIFPNTLAADVVPATIARFSQLNAEDQLALIWFAYLEMGKTLTIAAPGAASMQLAENALKEIQAMGPLQQTQAMCDLANRADTPLCRTYASWSPNIKLGFWYRLGELMEQGFVAPIPAGYQLSANANAVLATIQGLESGQQITVLRNAVVDMGFTAGKDGKRIAEPVVPPQDTASRTKVSIEGVTNATVLNYMDNLNANDFDTLIELFTSDGALQPPFQRPIVGKENVLRFFREECQNLKLIPERGVTEPAEDGFTQIKVTGKVQTPWFGGNVGMNIAWRFLLNPEGKIFFVAIDLLASPKELLNFARHHHHHH

Source Source

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

Entity 2 Entity 2 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 non-polymer

Description description	(3'R)-3'-hydroxy-beta,beta-caroten-4-one
Molecular weight formula_weight	566.9 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	263

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6. Fold Classification (SCOP + CATH) 24 domains

SCOP 2.08 (12 domains)

Domain ID domain_id	d5tuwa1
Class class	a — All alpha proteins
Fold Fold fold	a.175 — Orange carotenoid protein, N-terminal domain
Superfamily Superfamily superfamily	a.175.1 — Orange carotenoid protein, N-terminal domain
Family Family family	a.175.1.1 — Orange carotenoid protein, N-terminal domain

Domain ID domain_id	d5tuwa2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.17 — Cystatin-like
Superfamily Superfamily superfamily	d.17.4 — NTF2-like
Family Family family	d.17.4.0 — automated matches

Domain ID domain_id	d5tuwb1
Class class	a — All alpha proteins
Fold Fold fold	a.175 — Orange carotenoid protein, N-terminal domain
Superfamily Superfamily superfamily	a.175.1 — Orange carotenoid protein, N-terminal domain
Family Family family	a.175.1.1 — Orange carotenoid protein, N-terminal domain

Domain ID domain_id	d5tuwb2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.17 — Cystatin-like
Superfamily Superfamily superfamily	d.17.4 — NTF2-like
Family Family family	d.17.4.0 — automated matches

Domain ID domain_id	d5tuwc1
Class class	a — All alpha proteins
Fold Fold fold	a.175 — Orange carotenoid protein, N-terminal domain
Superfamily Superfamily superfamily	a.175.1 — Orange carotenoid protein, N-terminal domain
Family Family family	a.175.1.1 — Orange carotenoid protein, N-terminal domain

Domain ID domain_id	d5tuwc2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.17 — Cystatin-like
Superfamily Superfamily superfamily	d.17.4 — NTF2-like
Family Family family	d.17.4.0 — automated matches

Domain ID domain_id	d5tuwd1
Class class	a — All alpha proteins
Fold Fold fold	a.175 — Orange carotenoid protein, N-terminal domain
Superfamily Superfamily superfamily	a.175.1 — Orange carotenoid protein, N-terminal domain
Family Family family	a.175.1.1 — Orange carotenoid protein, N-terminal domain

Domain ID domain_id	d5tuwd2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.17 — Cystatin-like
Superfamily Superfamily superfamily	d.17.4 — NTF2-like
Family Family family	d.17.4.0 — automated matches

Domain ID domain_id	d5tuwe1
Class class	a — All alpha proteins
Fold Fold fold	a.175 — Orange carotenoid protein, N-terminal domain
Superfamily Superfamily superfamily	a.175.1 — Orange carotenoid protein, N-terminal domain
Family Family family	a.175.1.1 — Orange carotenoid protein, N-terminal domain

Domain ID domain_id	d5tuwe2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.17 — Cystatin-like
Superfamily Superfamily superfamily	d.17.4 — NTF2-like
Family Family family	d.17.4.0 — automated matches

Domain ID domain_id	d5tuwf1
Class class	a — All alpha proteins
Fold Fold fold	a.175 — Orange carotenoid protein, N-terminal domain
Superfamily Superfamily superfamily	a.175.1 — Orange carotenoid protein, N-terminal domain
Family Family family	a.175.1.1 — Orange carotenoid protein, N-terminal domain

Domain ID domain_id	d5tuwf2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.17 — Cystatin-like
Superfamily Superfamily superfamily	d.17.4 — NTF2-like
Family Family family	d.17.4.0 — automated matches

CATH v4.4 (12 domains)

Domain ID domain_id	5tuwA01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	2090 — orange carotenoid protein, domain 2
Homologous superfamily homologous superfamily	10 — Orange carotenoid-binding protein, N-terminal domain

Domain ID domain_id	5tuwA02
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	450 — Nuclear Transport Factor 2; Chain: A,
Homologous superfamily homologous superfamily	50 —

Domain ID domain_id	5tuwB01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	2090 — orange carotenoid protein, domain 2
Homologous superfamily homologous superfamily	10 — Orange carotenoid-binding protein, N-terminal domain

Domain ID domain_id	5tuwB02
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	450 — Nuclear Transport Factor 2; Chain: A,
Homologous superfamily homologous superfamily	50 —

Domain ID domain_id	5tuwC01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	2090 — orange carotenoid protein, domain 2
Homologous superfamily homologous superfamily	10 — Orange carotenoid-binding protein, N-terminal domain

Domain ID domain_id	5tuwC02
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	450 — Nuclear Transport Factor 2; Chain: A,
Homologous superfamily homologous superfamily	50 —

Domain ID domain_id	5tuwD01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	2090 — orange carotenoid protein, domain 2
Homologous superfamily homologous superfamily	10 — Orange carotenoid-binding protein, N-terminal domain

Domain ID domain_id	5tuwD02
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	450 — Nuclear Transport Factor 2; Chain: A,
Homologous superfamily homologous superfamily	50 —

Domain ID domain_id	5tuwE01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	2090 — orange carotenoid protein, domain 2
Homologous superfamily homologous superfamily	10 — Orange carotenoid-binding protein, N-terminal domain

Domain ID domain_id	5tuwE02
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	450 — Nuclear Transport Factor 2; Chain: A,
Homologous superfamily homologous superfamily	50 —

Domain ID domain_id	5tuwF01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	2090 — orange carotenoid protein, domain 2
Homologous superfamily homologous superfamily	10 — Orange carotenoid-binding protein, N-terminal domain

Domain ID domain_id	5tuwF02
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	450 — Nuclear Transport Factor 2; Chain: A,
Homologous superfamily homologous superfamily	50 —

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Unit-cell length a length_a	82.947 Å
Unit-cell length b length_b	82.914 Å
Unit-cell length c length_c	87.438 Å
Unit-cell angle α angle_alpha	89.79 °
Unit-cell angle β angle_beta	89.91 °
Unit-cell angle γ angle_gamma	60.04 °
Molecules per unit cell Z z_pdb	6

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Resolution resolution	2.302 Å
Low-resolution limit resolution_low	41.490 Å
R factor r_factor	0.1859
R_work r_work	0.1846
R_free r_free	0.2386

Crystal structure of Orange Carotenoid Protein with partial loss of 3'OH Echinenone chromophore

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

Orange carotenoid-binding protein

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

5tuw__assembly_1__model_1

5tuw__assembly_1__model_1 | I(q)

5tuw__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) 24 domains

SCOP 2.08 (12 domains)

CATH v4.4 (12 domains)

7. Citations (1)

Crystal structure of Orange Carotenoid Protein with partial loss of 3'OH Echinenone chromophore

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

Orange carotenoid-binding protein

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

5tuw__assembly_1__model_1

5tuw__assembly_1__model_1 | I(q)

5tuw__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) 24 domains

SCOP 2.08 (12 domains)

CATH v4.4 (12 domains)

7. Citations (1)