2vml

The monoclinic structure of phycocyanin from Gloeobacter violaceus

Method: X-RAY DIFFRACTION

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

PHYCOCYANIN ALPHA CHAIN

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 12	PHYCOCYANIN BETA CHAIN × 6 （Q7M7C7） PHYCOCYANOBILIN × 18 water × 12	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q7M7F7_GLOVI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–162； UniProt 1–162 Author chain C； PDBConstruct 1–162； UniProt 1–162 Author chain E； PDBConstruct 1–162； UniProt 1–162 Author chain G； PDBConstruct 1–162； UniProt 1–162 Author chain I； PDBConstruct 1–162； UniProt 1–162 Author chain K； PDBConstruct 1–162； UniProt 1–162

PHYCOCYANIN BETA CHAIN

OrganismNot specified

UniProt Q7M7C7

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 12	PHYCOCYANIN ALPHA CHAIN × 6 （Q7M7F7） PHYCOCYANOBILIN × 18 water × 12	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q7M7C7_GLOVI
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–172； UniProt 1–172 Author chain D； PDBConstruct 1–172； UniProt 1–172 Author chain F； PDBConstruct 1–172； UniProt 1–172 Author chain H； PDBConstruct 1–172； UniProt 1–172 Author chain J； PDBConstruct 1–172； UniProt 1–172 Author chain L； PDBConstruct 1–172； UniProt 1–172

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	2vml
Deposition date deposition_date	2008-01-28
Structure title title	The monoclinic structure of phycocyanin from Gloeobacter violaceus
Keywords keywords	PHOTOSYNTHESIS, LIGHT-HARVESTING, ELECTRON TRANSPORT, TRANSPORT, CHROMOPHORE, BILE PIGMENT, PHYCOBILISOME; 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.

2vml__assembly_1__model_1

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

Download this curve (.dat)

2vml__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2vml__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	41.65 Å
Rg (electron density)	40.81 Å
Total Rg	41.22 Å
Atom count	15990
Residues	2004
Excluded volume	284330 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2vml__assembly_1__model_1`	dodecameric （12）	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	PHYCOCYANIN ALPHA CHAIN
Molecular weight formula_weight	17679.9 kDa
Source method src_method	nat
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C,E,G,I,K
Atom count atom_count	16700

MKTVITEVIASADSQGRFLNNTELQAANGRFQRATASMEAARALTSNADSLVKGAVQEVYNKFPYLTQPGQMGYGDTNQAKCARDISHYLRFITYSLVAGGTGPLDDYIVAGLREVNRTFNLSPSWYIEALKHIKGKVGSQLSGQPLTEANAYIDYCINALS

Entity 2 Entity 2 polymer

Description description	PHYCOCYANIN BETA CHAIN
Molecular weight formula_weight	18479.0 kDa
Source method src_method	nat
Copy count entity_count	6

Polymer Polymer

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

MQDAFTKAIVAADLRGSFLSEQELNQLTNLVKESNKRLDAVNAITGNAAEIISDAAHKLFAEQTDLIRPGGNAYPNRRMAACLRDMEIILRYVSYALLAGDASVLEDRCLNGLKETYVALGTPTRSVARAVQLMKETAIGYVNSPSGVTRGDCSALVNEAATYFDKAAASIA

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	18

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	710

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6. Fold Classification (SCOP + CATH) 24 domains

SCOP 2.08 (12 domains)

Domain ID domain_id	d2vmla_
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	d2vmlb_
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	d2vmlc_
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	d2vmld_
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	d2vmle_
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	d2vmlf_
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	d2vmlg_
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	d2vmlh_
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	d2vmli_
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	d2vmlj_
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	d2vmlk_
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	d2vmll_
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 (12 domains)

Domain ID domain_id	2vmlA00
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	2vmlB00
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	2vmlC00
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	2vmlD00
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	2vmlE00
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	2vmlF00
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	2vmlG00
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	2vmlH00
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	2vmlI00
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	2vmlJ00
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	2vmlK00
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	2vmlL00
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	86.877 Å
Unit-cell length b length_b	142.040 Å
Unit-cell length c length_c	115.313 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	107.65 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	12

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

Resolution resolution	2.400 Å
Low-resolution limit resolution_low	109.760 Å
R factor r_factor	0.1940
R_work r_work	0.1920
R_free r_free	0.2180

The monoclinic structure of phycocyanin from Gloeobacter violaceus

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

PHYCOCYANIN ALPHA CHAIN

State in the Current Structure

Other States of the Same Protein in the Database

PHYCOCYANIN BETA CHAIN

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

2vml__assembly_1__model_1

2vml__assembly_1__model_1 | I(q)

2vml__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

Entity 2 Entity 2 polymer

Polymer 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)

The monoclinic structure of phycocyanin from Gloeobacter violaceus

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

PHYCOCYANIN ALPHA CHAIN

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

PHYCOCYANIN BETA CHAIN

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

2vml__assembly_1__model_1

2vml__assembly_1__model_1 | I(q)

2vml__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

Entity 2 Entity 2 polymer

Polymer 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)