SAXSdb — 2vea

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

PHYTOCHROME-LIKE PROTEIN CPH1

SYNECHOCYSTIS SP. PCC 6803

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	PHYCOCYANOBILIN × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PHY1_SYNY3
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–514； UniProt 1–514

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	2vea
Deposition date deposition_date	2007-10-18
Structure title title	The complete sensory module of the cyanobacterial phytochrome Cph1 in the Pr-state.
Keywords keywords	;ARGININE FINGER, PHOSPHORYLATION, TANDEM GAF DOMAIN, KNOT, KINASE, RECEPTOR, PAS DOMAIN, CHROMOPHORE, SENSORY TRANSDUCTION, PHOTORECEPTOR PROTEIN, BILIN-LIKE CHROMOPHORE, PHYTOCHROME, TRANSFERASE, PHOTORECEPTOR ;; TRANSFERASE
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.

2vea__assembly_1__model_1

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

Download this curve (.dat)

2vea__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2vea__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	33.85 Å
Rg (electron density)	32.91 Å
Total Rg	33.54 Å
Atom count	7954
Residues	1000
Excluded volume	141590 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2vea__assembly_1__model_1`	dimeric （2）	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 (3)

Entity 1 Entity 1 polymer

Description description	PHYTOCHROME-LIKE PROTEIN CPH1
Molecular weight formula_weight	58765.5 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	4022

MATTVQLSDQSLRQLETLAIHTAHLIQPHGLVVVLQEPDLTISQISANCTGILGRSPEDLLGRTLGEVFDSFQIDPIQSRLTAGQISSLNPSKLWARVMGDDFVIFDGVFHRNSDGLLVCELEPAYTSDNLPFLGFYHMANAALNRLRQQANLRDFYDVIVEEVRRMTGFDRVMLYRFDENNHGDVIAEDKRDDMEPYLGLHYPESDIPQPARRLFIHNPIRVIPDVYGVAVPLTPAVNPSTNRAVDLTESILRSAYHCHLTYLKNMGVGASLTISLIKDGHLWGLIACHHQTPKVIPFELRKACEFFGRVVFSNISAQEDTETFDYRVQLAEHEAVLLDKMTTAADFVEGLTNHPDRLLGLTGSQGAAICFGEKLILVGETPDEKAVQYLLQWLENREVQDVFFTSSLSQIYPDAVNFKSVASGLLAIPIARHNFLLWFRPEVLQTVNWGGDPNHAYEATQEDGKIELHPRQSFDLWKEIVRLQSLPWQSVEIQSALALKKAIVNLILRQAEEHHHHHH

Source Source

Source organism organism	SYNECHOCYSTIS SP. PCC 6803
NCBI taxonomy ID ncbi_taxonomy_id	1148
Host organism host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 non-polymer

Description description	PHYCOCYANOBILIN
Molecular weight formula_weight	588.7 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	29

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6. Fold Classification (SCOP + CATH) 7 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d2veaa1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.110 — Profilin-like
Superfamily Superfamily superfamily	d.110.2 — GAF domain-like
Family Family family	d.110.2.1 — GAF domain

Domain ID domain_id	d2veaa2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.110 — Profilin-like
Superfamily Superfamily superfamily	d.110.2 — GAF domain-like
Family Family family	d.110.2.4 — Phytochrome-specific domain

Domain ID domain_id	d2veaa3
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.110 — Profilin-like
Superfamily Superfamily superfamily	d.110.3 — PYP-like sensor domain (PAS domain)
Family Family family	d.110.3.9 — BphP N-terminal domain-like

Domain ID domain_id	d2veaa4
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (3 domains)

Domain ID domain_id	2veaA01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	450 — Beta-Lactamase
Homologous superfamily homologous superfamily	40 — GAF domain

Domain ID domain_id	2veaA02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	450 — Beta-Lactamase
Homologous superfamily homologous superfamily	20 — PAS domain

Domain ID domain_id	2veaA03
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	450 — Beta-Lactamase
Homologous superfamily homologous superfamily	270 — PHY domain

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Unit-cell length a length_a	77.180 Å
Unit-cell length b length_b	77.180 Å
Unit-cell length c length_c	249.000 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	8

Space group space_group	P 43 21 2
Space-group number int_tables_number	96
Crystal system crystal_system	—

Resolution resolution	2.210 Å
Low-resolution limit resolution_low	24.680 Å
R factor r_factor	0.2450
R_work r_work	0.2440
R_free r_free	0.2710

The complete sensory module of the cyanobacterial phytochrome Cph1 in the Pr-state.

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

PHYTOCHROME-LIKE PROTEIN CPH1

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

2vea__assembly_1__model_1

2vea__assembly_1__model_1 | I(q)

2vea__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 7 domains

SCOP 2.08 (4 domains)

CATH v4.4 (3 domains)

7. Citations (1)

The complete sensory module of the cyanobacterial phytochrome Cph1 in the Pr-state.

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

PHYTOCHROME-LIKE PROTEIN CPH1

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

2vea__assembly_1__model_1

2vea__assembly_1__model_1 | I(q)

2vea__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 7 domains

SCOP 2.08 (4 domains)

CATH v4.4 (3 domains)

7. Citations (1)