SAXSdb — 2iyg

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

APPA, ANTIREPRESSOR OF PPSR, SENSOR OF BLUE LIGHT

RHODOBACTER SPHAEROIDES

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 4	FLAVIN MONONUCLEOTIDE × 4 (2R,3S)-1,4-DIMERCAPTOBUTANE-2,3-DIOL × 2 2,3-DIHYDROXY-1,4-DITHIOBUTANE × 2 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q3J677_RHOS4
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–124； UniProt 1–124 Author chain B； PDBConstruct 1–124； UniProt 1–124

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	2iyg
Deposition date deposition_date	2006-07-17
Structure title title	Dark state structure of the BLUF domain of the rhodobacterial protein AppA
Keywords keywords	SIGNAL TRANSDUCTION; SIGNAL TRANSDUCTION
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.

2iyg__assembly_1__model_1

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

Download this curve (.dat)

2iyg__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2iyg__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	23.80 Å
Rg (electron density)	22.58 Å
Total Rg	23.53 Å
Atom count	3556
Residues	434
Excluded volume	62434 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2iyg__assembly_1__model_1`	tetrameric （4）	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 (5)

Entity 1 Entity 1 polymer

Description description	APPA, ANTIREPRESSOR OF PPSR, SENSOR OF BLUE LIGHT
Molecular weight formula_weight	13919.7 kDa
Mutation mutation	YES
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	1838

MQHDLEADVTMTGSDLVSCSYRSLAAPDLTLRDLLDIVETSQAHNARAQLTGALFYSQGVFFQWLEGRPAAVAEVMTHIQRDRRHSNVEILAEEPIAKRRFAGWHMQLSCSEADMRSLGLAESR

Source Source

Source organism organism	RHODOBACTER SPHAEROIDES
NCBI taxonomy ID ncbi_taxonomy_id	1063
Host organism host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 non-polymer

Description description	FLAVIN MONONUCLEOTIDE
Molecular weight formula_weight	456.3 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	(2R,3S)-1,4-DIMERCAPTOBUTANE-2,3-DIOL
Molecular weight formula_weight	154.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	2,3-DIHYDROXY-1,4-DITHIOBUTANE
Molecular weight formula_weight	154.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	60

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6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d2iyga_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.10 — Acylphosphatase/BLUF domain-like
Family Family family	d.58.10.2 — BLUF domain

Domain ID domain_id	d2iygb_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.10 — Acylphosphatase/BLUF domain-like
Family Family family	d.58.10.2 — BLUF domain

CATH v4.4 (2 domains)

Domain ID domain_id	2iygA00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	100 —

Domain ID domain_id	2iygB00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	100 —

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Unit-cell length a length_a	127.710 Å
Unit-cell length b length_b	127.710 Å
Unit-cell length c length_c	65.350 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	24

Space group space_group	P 65 2 2
Space-group number int_tables_number	179
Crystal system crystal_system	—

Resolution resolution	2.300 Å
Low-resolution limit resolution_low	9.990 Å
R factor r_factor	0.2090
R_work r_work	0.2080
R_free r_free	0.2330

Dark state structure of the BLUF domain of the rhodobacterial protein AppA

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

APPA, ANTIREPRESSOR OF PPSR, SENSOR OF BLUE LIGHT

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

2iyg__assembly_1__model_1

2iyg__assembly_1__model_1 | I(q)

2iyg__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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)

Dark state structure of the BLUF domain of the rhodobacterial protein AppA

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

APPA, ANTIREPRESSOR OF PPSR, SENSOR OF BLUE LIGHT

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

2iyg__assembly_1__model_1

2iyg__assembly_1__model_1 | I(q)

2iyg__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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)