SAXSdb — 5j4e

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

Sensory box protein

Pseudomonas putida

State in the Current Structure

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

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q88E39_PSEPK
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 21–162； UniProt 1–142 Author chain B； PDBConstruct 21–162； UniProt 1–142 Author chain C； PDBConstruct 21–162； UniProt 1–142 Author chain D； PDBConstruct 21–162； UniProt 1–142

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	5j4e
Deposition date deposition_date	2016-04-01
Structure title title	Crystal structures reveal signaling states of a short blue light photoreceptor protein PpSB1-LOV (Photoexcited state)
Keywords keywords	Signaling Protein, LOV domain; 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.

5j4e__assembly_1__model_1

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

Download this curve (.dat)

5j4e__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5j4e__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	20.74 Å
Rg (electron density)	19.52 Å
Total Rg	20.32 Å
Atom count	2041
Residues	267
Excluded volume	35702 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5j4e__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`5j4e__assembly_2__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 (2)

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6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d5j4ea_
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.110.3.0 — automated matches

Domain ID domain_id	d5j4eb_
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.110.3.0 — automated matches

Domain ID domain_id	d5j4ec_
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.110.3.0 — automated matches

Domain ID domain_id	d5j4ed_
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.110.3.0 — automated matches

CATH v4.4 (4 domains)

Domain ID domain_id	5j4eA00
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	5j4eB00
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	5j4eC00
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	5j4eD00
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	102.409 Å
Unit-cell length b length_b	71.080 Å
Unit-cell length c length_c	91.369 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	91.02 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	16

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	2.670 Å
Low-resolution limit resolution_low	45.677 Å
R factor r_factor	0.1898
R_work r_work	0.1860
R_free r_free	0.2608

Description description	Sensory box protein
Molecular weight formula_weight	18617.8 kDa
Source method src_method	man
Copy count entity_count	4

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	4159

Crystal structures reveal signaling states of a short blue light photoreceptor protein PpSB1-LOV (Photoexcited state)

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

Sensory box 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

5j4e__assembly_1__model_1

5j4e__assembly_1__model_1 | I(q)

5j4e__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)

Source organism organism	Pseudomonas putida
NCBI taxonomy ID ncbi_taxonomy_id	303
Host organism host_organism	Escherichia coli

Description description	FLAVIN MONONUCLEOTIDE
Molecular weight formula_weight	456.3 kDa
Source method src_method	syn
Copy count entity_count	4

Crystal structures reveal signaling states of a short blue light photoreceptor protein PpSB1-LOV (Photoexcited state)

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

Sensory box 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

5j4e__assembly_1__model_1

5j4e__assembly_1__model_1 | I(q)

5j4e__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)