SAXSdb — 3x15

▼

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

Cytochrome c552

Aquifex aeolicus VF5

State in the Current Structure

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

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	O67504_AQUAE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–87； UniProt 18–104 Author chain D； PDBConstruct 1–87； UniProt 18–104 Author chain G； PDBConstruct 1–87； UniProt 18–104 Author chain J； PDBConstruct 1–87； UniProt 18–104

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	3x15
Deposition date deposition_date	2014-10-29
Structure title title	Dimeric Aquifex aeolicus cytochrome c555
Keywords keywords	Electron Transport; ELECTRON TRANSPORT
Experimental Method method	X-RAY DIFFRACTION

▼

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.

3x15__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

3x15__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3x15__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	19.51 Å
Rg (electron density)	18.86 Å
Total Rg	19.68 Å
Atom count	1382
Residues	174
Excluded volume	25107 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3x15__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3x15__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Cytochrome c552
Molecular weight formula_weight	9264.8 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,D,G,J
Atom count atom_count	3316

ADGKAIFQQKGCGSCHQANVDTVGPSLKKIAQAYAGKEDQLIKFLKGEAPAIVDPAKEAIMKPQLTMLKGLSDAELKALADFILSHK

Source Source

Source organism organism	Aquifex aeolicus VF5
NCBI taxonomy ID ncbi_taxonomy_id	224324
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	HEME C
Molecular weight formula_weight	618.5 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	469

▼

6. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d3x15a_
Class class	a — All alpha proteins
Fold Fold fold	a.3 — Cytochrome c
Superfamily Superfamily superfamily	a.3.1 — Cytochrome c
Family Family family	a.3.1.0 — automated matches

Domain ID domain_id	d3x15d_
Class class	a — All alpha proteins
Fold Fold fold	a.3 — Cytochrome c
Superfamily Superfamily superfamily	a.3.1 — Cytochrome c
Family Family family	a.3.1.0 — automated matches

Domain ID domain_id	d3x15g_
Class class	a — All alpha proteins
Fold Fold fold	a.3 — Cytochrome c
Superfamily Superfamily superfamily	a.3.1 — Cytochrome c
Family Family family	a.3.1.0 — automated matches

Domain ID domain_id	d3x15j_
Class class	a — All alpha proteins
Fold Fold fold	a.3 — Cytochrome c
Superfamily Superfamily superfamily	a.3.1 — Cytochrome c
Family Family family	a.3.1.0 — automated matches

CATH v4.4 (1 domains)

Domain ID domain_id	3x15G01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	760 — Cytochrome Bc1 Complex; Chain D, domain 2
Homologous superfamily homologous superfamily	10 — Cytochrome c-like domain

▶

Unit-cell length a length_a	57.591 Å
Unit-cell length b length_b	54.464 Å
Unit-cell length c length_c	65.403 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	114.47 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

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

Resolution resolution	1.600 Å
Low-resolution limit resolution_low	33.121 Å
R factor r_factor	0.1538
R_work r_work	0.1505
R_free r_free	0.2138

Dimeric Aquifex aeolicus cytochrome c555

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

Cytochrome c552

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

3x15__assembly_2__model_1

3x15__assembly_2__model_1 | I(q)

3x15__assembly_2__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) 5 domains

SCOP 2.08 (4 domains)

CATH v4.4 (1 domains)

7. Citations (1)

Dimeric Aquifex aeolicus cytochrome c555

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

Cytochrome c552

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

3x15__assembly_2__model_1

3x15__assembly_2__model_1 | I(q)

3x15__assembly_2__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) 5 domains

SCOP 2.08 (4 domains)

CATH v4.4 (1 domains)

7. Citations (1)