SAXSdb — 4bbu

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

PHOTOACTIVE YELLOW PROTEIN

HALORHODOSPIRA HALOPHILA

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	;4'-HYDROXYCINNAMIC ACID ; × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PYP_HALHA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–125； UniProt 1–125

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	4bbu
Deposition date deposition_date	2012-09-27
Structure title title	The PR2 Photocycle Intermediate of Photoactive Yellow Protein
Keywords keywords	PHOTORECEPTOR, LIGHT SENSOR, CHROMOPHORE, PHOTORECEPTOR PROTEIN, RECEPTOR, SENSORY TRANSDUCTION, SIGNALING PROTEIN, PAS, LOV; SIGNALING 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.

4bbu__assembly_1__model_1

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

Download this curve (.dat)

4bbu__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4bbu__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	14.85 Å
Rg (electron density)	13.26 Å
Total Rg	14.65 Å
Atom count	987
Residues	125
Excluded volume	17495 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4bbu__assembly_1__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 (3)

Entity 1 Entity 1 polymer

Description description	PHOTOACTIVE YELLOW PROTEIN
Molecular weight formula_weight	13888.6 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	1126

MEHVAFGSEDIENTLAKMDDGQLDGLAFGAIQLDGDGNILQYNAAEGDITGRDPKQVIGKNFFKDVAPCTDSPEFYGKFKEGVASGNLNTMFEYTFDYQMTPTKVKVHMKKALSGDSYWVFVKRV

Source Source

Source organism organism	HALORHODOSPIRA HALOPHILA
NCBI taxonomy ID ncbi_taxonomy_id	1053
Host organism host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 non-polymer

Description description	;4'-HYDROXYCINNAMIC ACID ;
Molecular weight formula_weight	164.2 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	139

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6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d4bbua_
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.110.3.1 — PYP-like

CATH v4.4 (1 domains)

Domain ID domain_id	4bbuA00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	450 — Beta-Lactamase
Homologous superfamily homologous superfamily	20 — PAS domain

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Unit-cell length a length_a	66.833 Å
Unit-cell length b length_b	66.833 Å
Unit-cell length c length_c	40.947 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	6

Space group space_group	P 63
Space-group number int_tables_number	173
Crystal system crystal_system	—

Resolution resolution	1.600 Å
Low-resolution limit resolution_low	13.285 Å
R factor r_factor	0.1667
R_work r_work	0.1645
R_free r_free	0.2184

The PR2 Photocycle Intermediate of Photoactive Yellow Protein

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

PHOTOACTIVE YELLOW 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

4bbu__assembly_1__model_1

4bbu__assembly_1__model_1 | I(q)

4bbu__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) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

7. Citations (1)

The PR2 Photocycle Intermediate of Photoactive Yellow Protein

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

PHOTOACTIVE YELLOW 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

4bbu__assembly_1__model_1

4bbu__assembly_1__model_1 | I(q)

4bbu__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) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

7. Citations (1)