3dbj

Allophycocyanin from Thermosynechococcus vulcanus

Method: X-RAY DIFFRACTION

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

Allophycocyanin

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 6	Allophycocyanin × 3 （B3VNK3） PHYCOCYANOBILIN × 6 water × 6	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 6	Allophycocyanin × 3 （B3VNK3） PHYCOCYANOBILIN × 6 water × 6	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 6	Allophycocyanin × 3 （B3VNK3） PHYCOCYANOBILIN × 6 water × 6	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 6	Allophycocyanin × 3 （B3VNK3） PHYCOCYANOBILIN × 6 water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	B3VNK2_THEVL
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–161； UniProt 1–161 Author chain C； PDBConstruct 1–161； UniProt 1–161 Author chain E； PDBConstruct 1–161； UniProt 1–161 Author chain G； PDBConstruct 1–161； UniProt 1–161

Allophycocyanin

OrganismNot specified

UniProt B3VNK3

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 6	Allophycocyanin × 3 （B3VNK2） PHYCOCYANOBILIN × 6 water × 6	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 6	Allophycocyanin × 3 （B3VNK2） PHYCOCYANOBILIN × 6 water × 6	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 6	Allophycocyanin × 3 （B3VNK2） PHYCOCYANOBILIN × 6 water × 6	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 6	Allophycocyanin × 3 （B3VNK2） PHYCOCYANOBILIN × 6 water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	B3VNK3_THEVL
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–161； UniProt 1–161 Author chain D； PDBConstruct 1–161； UniProt 1–161 Author chain F； PDBConstruct 1–161； UniProt 1–161 Author chain H； PDBConstruct 1–161； UniProt 1–161

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	3dbj
Deposition date deposition_date	2008-06-01
Structure title title	Allophycocyanin from Thermosynechococcus vulcanus
Keywords keywords	phycobilisome, light harvesting, photosynthesis, energy transfer, cyanobacteria; PHOTOSYNTHESIS
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.

3dbj__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

3dbj__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3dbj__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	39.42 Å
Rg (electron density)	38.65 Å
Total Rg	39.14 Å
Atom count	7566
Residues	960
Excluded volume	135360 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3dbj__assembly_1__model_1`	hexameric （6）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3dbj__assembly_2__model_1`	hexameric （6）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`3dbj__assembly_3__model_1`	hexameric （6）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`3dbj__assembly_4__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	Allophycocyanin
Molecular weight formula_weight	17555.9 kDa
Source method src_method	nat
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C,E,G
Atom count atom_count	10448

MSVVTKSIVNADAEARYLSPGELDRIKNFVSTGERRLRIAQTLTENRERIVKQAGDQLFQKRPDVVSPGGNAYGEEMTATCLRDLDYYLRLVTYGIVAGDVTPIEEIGLVGVREMYNSLGTPIPAVAEGIRAMKNVACSLLSAEDAAEAGSYFDFVIGAMQ

Entity 2 Entity 2 polymer

Description description	Allophycocyanin
Molecular weight formula_weight	17388.9 kDa
Source method src_method	nat
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,D,F,H

MQDAITAVINASDVQGKYLDTAAMEKLKAYFATGELRVRAASVISANAANIVKEAVAKSLLYSDITRPGGNMYTTRRYAACIRDLDYYLRYATYAMLAGDPSILDERVLNGLKETYNSLGVPIAATVQAIQAMKEVTASLVGADAGKEMGIYFDYICSGLS

Entity 3 Entity 3 non-polymer

Description description	PHYCOCYANOBILIN
Molecular weight formula_weight	588.7 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	360

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6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d3dbja_
Class class	a — All alpha proteins
Fold Fold fold	a.1 — Globin-like
Superfamily Superfamily superfamily	a.1.1 — Globin-like
Family Family family	a.1.1.3 — Phycocyanin-like phycobilisome proteins

Domain ID domain_id	d3dbjb_
Class class	a — All alpha proteins
Fold Fold fold	a.1 — Globin-like
Superfamily Superfamily superfamily	a.1.1 — Globin-like
Family Family family	a.1.1.3 — Phycocyanin-like phycobilisome proteins

Domain ID domain_id	d3dbjc_
Class class	a — All alpha proteins
Fold Fold fold	a.1 — Globin-like
Superfamily Superfamily superfamily	a.1.1 — Globin-like
Family Family family	a.1.1.3 — Phycocyanin-like phycobilisome proteins

Domain ID domain_id	d3dbjd_
Class class	a — All alpha proteins
Fold Fold fold	a.1 — Globin-like
Superfamily Superfamily superfamily	a.1.1 — Globin-like
Family Family family	a.1.1.3 — Phycocyanin-like phycobilisome proteins

Domain ID domain_id	d3dbje_
Class class	a — All alpha proteins
Fold Fold fold	a.1 — Globin-like
Superfamily Superfamily superfamily	a.1.1 — Globin-like
Family Family family	a.1.1.3 — Phycocyanin-like phycobilisome proteins

Domain ID domain_id	d3dbjf_
Class class	a — All alpha proteins
Fold Fold fold	a.1 — Globin-like
Superfamily Superfamily superfamily	a.1.1 — Globin-like
Family Family family	a.1.1.3 — Phycocyanin-like phycobilisome proteins

Domain ID domain_id	d3dbjg_
Class class	a — All alpha proteins
Fold Fold fold	a.1 — Globin-like
Superfamily Superfamily superfamily	a.1.1 — Globin-like
Family Family family	a.1.1.3 — Phycocyanin-like phycobilisome proteins

Domain ID domain_id	d3dbjh_
Class class	a — All alpha proteins
Fold Fold fold	a.1 — Globin-like
Superfamily Superfamily superfamily	a.1.1 — Globin-like
Family Family family	a.1.1.3 — Phycocyanin-like phycobilisome proteins

CATH v4.4 (8 domains)

Domain ID domain_id	3dbjA00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	490 — Globin-like
Homologous superfamily homologous superfamily	20 — Phycocyanins

Domain ID domain_id	3dbjB00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	490 — Globin-like
Homologous superfamily homologous superfamily	20 — Phycocyanins

Domain ID domain_id	3dbjC00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	490 — Globin-like
Homologous superfamily homologous superfamily	20 — Phycocyanins

Domain ID domain_id	3dbjD00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	490 — Globin-like
Homologous superfamily homologous superfamily	20 — Phycocyanins

Domain ID domain_id	3dbjE00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	490 — Globin-like
Homologous superfamily homologous superfamily	20 — Phycocyanins

Domain ID domain_id	3dbjF00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	490 — Globin-like
Homologous superfamily homologous superfamily	20 — Phycocyanins

Domain ID domain_id	3dbjG00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	490 — Globin-like
Homologous superfamily homologous superfamily	20 — Phycocyanins

Domain ID domain_id	3dbjH00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	490 — Globin-like
Homologous superfamily homologous superfamily	20 — Phycocyanins

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Unit-cell length a length_a	102.597 Å
Unit-cell length b length_b	102.597 Å
Unit-cell length c length_c	128.860 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	P 3
Space-group number int_tables_number	143
Crystal system crystal_system	—

Resolution resolution	2.900 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	—
R_work r_work	0.2117
R_free r_free	0.2695

Allophycocyanin from Thermosynechococcus vulcanus

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

Allophycocyanin

State in the Current Structure

Other States of the Same Protein in the Database

Allophycocyanin

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

3dbj__assembly_2__model_1

3dbj__assembly_2__model_1 | I(q)

3dbj__assembly_2__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

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

CATH v4.4 (8 domains)

7. Citations (1)

Allophycocyanin from Thermosynechococcus vulcanus

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

Allophycocyanin

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Allophycocyanin

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

3dbj__assembly_2__model_1

3dbj__assembly_2__model_1 | I(q)

3dbj__assembly_2__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

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

CATH v4.4 (8 domains)

7. Citations (1)