SAXSdb — 5gyr

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

;Cytochrome c' ;

Allochromatium vinosum (strain ATCC 17899 / DSM 180 / NBRC 103801 / NCIMB 10441 / D)

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 4	HEME C × 4 water × 4	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 4	HEME C × 4 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CYCP_ALLVD
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–131； UniProt 24–154 Author chain B； PDBConstruct 1–131； UniProt 24–154 Author chain E； PDBConstruct 1–131； UniProt 24–154 Author chain F； PDBConstruct 1–131； UniProt 24–154 Author chain I； PDBConstruct 1–131； UniProt 24–154 Author chain J； PDBConstruct 1–131； UniProt 24–154 Author chain M； PDBConstruct 1–131； UniProt 24–154 Author chain N； PDBConstruct 1–131； UniProt 24–154

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	5gyr
Deposition date deposition_date	2016-09-23
Structure title title	Tetrameric Allochromatium vinosum cytochrome c'
Keywords keywords	ELECTRON TRANSPORT; ELECTRON TRANSPORT
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.

5gyr__assembly_1__model_1

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

Download this curve (.dat)

5gyr__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5gyr__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	28.00 Å
Rg (electron density)	27.53 Å
Total Rg	28.17 Å
Atom count	4040
Residues	524
Excluded volume	71344 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5gyr__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`5gyr__assembly_2__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 (3)

Entity 1 Entity 1 polymer

Description description	;Cytochrome c' ;
Molecular weight formula_weight	13806.4 kDa
Source method src_method	man
Copy count entity_count	8

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,E,F,I,J,M,N
Atom count atom_count	8888

AGLSPEEQIETRQAGYEFMGWNMGKIKANLEGEYNAAQVEAAANVIAAIANSGMGALYGPGTDKNVGDVKTRVKPEFFQNMEDVGKIAREFVGAANTLAEVAATGEAEAVKTAFGDVGAACKSCHEKYRAK

Source Source

Source organism organism	Allochromatium vinosum (strain ATCC 17899 / DSM 180 / NBRC 103801 / NCIMB 10441 / D)
NCBI taxonomy ID ncbi_taxonomy_id	572477
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	8

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	808

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6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d5gyra_
Class class	a — All alpha proteins
Fold Fold fold	a.24 — Four-helical up-and-down bundle
Superfamily Superfamily superfamily	a.24.3 — Cytochromes
Family Family family	a.24.3.2 — Cytochrome c'-like

Domain ID domain_id	d5gyrb_
Class class	a — All alpha proteins
Fold Fold fold	a.24 — Four-helical up-and-down bundle
Superfamily Superfamily superfamily	a.24.3 — Cytochromes
Family Family family	a.24.3.2 — Cytochrome c'-like

Domain ID domain_id	d5gyre_
Class class	a — All alpha proteins
Fold Fold fold	a.24 — Four-helical up-and-down bundle
Superfamily Superfamily superfamily	a.24.3 — Cytochromes
Family Family family	a.24.3.2 — Cytochrome c'-like

Domain ID domain_id	d5gyrf_
Class class	a — All alpha proteins
Fold Fold fold	a.24 — Four-helical up-and-down bundle
Superfamily Superfamily superfamily	a.24.3 — Cytochromes
Family Family family	a.24.3.2 — Cytochrome c'-like

Domain ID domain_id	d5gyri_
Class class	a — All alpha proteins
Fold Fold fold	a.24 — Four-helical up-and-down bundle
Superfamily Superfamily superfamily	a.24.3 — Cytochromes
Family Family family	a.24.3.2 — Cytochrome c'-like

Domain ID domain_id	d5gyrj_
Class class	a — All alpha proteins
Fold Fold fold	a.24 — Four-helical up-and-down bundle
Superfamily Superfamily superfamily	a.24.3 — Cytochromes
Family Family family	a.24.3.2 — Cytochrome c'-like

Domain ID domain_id	d5gyrm_
Class class	a — All alpha proteins
Fold Fold fold	a.24 — Four-helical up-and-down bundle
Superfamily Superfamily superfamily	a.24.3 — Cytochromes
Family Family family	a.24.3.2 — Cytochrome c'-like

Domain ID domain_id	d5gyrn_
Class class	a — All alpha proteins
Fold Fold fold	a.24 — Four-helical up-and-down bundle
Superfamily Superfamily superfamily	a.24.3 — Cytochromes
Family Family family	a.24.3.2 — Cytochrome c'-like

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Unit-cell length a length_a	82.949 Å
Unit-cell length b length_b	48.620 Å
Unit-cell length c length_c	130.550 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	92.28 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	16

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	41.400 Å
R factor r_factor	0.2055
R_work r_work	0.2041
R_free r_free	0.2323

Tetrameric Allochromatium vinosum cytochrome c'

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

;Cytochrome c' ;

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

5gyr__assembly_1__model_1

5gyr__assembly_1__model_1 | I(q)

5gyr__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) 8 domains

SCOP 2.08 (8 domains)

7. Citations (1)

Tetrameric Allochromatium vinosum cytochrome c'

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

;Cytochrome c' ;

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

5gyr__assembly_1__model_1

5gyr__assembly_1__model_1 | I(q)

5gyr__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) 8 domains

SCOP 2.08 (8 domains)

7. Citations (1)