SAXSdb — 5xed

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

Cytochrome c-551,Cytochrome c-552

Hydrogenobacter thermophilus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	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	CY551_PSEAE
Isoform	—
PDB entities	1, 2
Chains and sequence ranges	Author chain A； PDBConstruct 1–20； UniProt 23–42 Author chain C； PDBConstruct 19–80； UniProt 43–104

Cytochrome c-551,Cytochrome c-552

Hydrogenobacter thermophilus

UniProt P15452

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	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	CY552_HYDTT
Isoform	—
PDB entities	1, 2
Chains and sequence ranges	Author chain A； PDBConstruct 21–82； UniProt 37–98 Author chain C； PDBConstruct 1–18； UniProt 19–36

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	5xed
Deposition date deposition_date	2017-04-04
Structure title title	Heterodimer constructed from M61A PA cyt c551-HT cyt c552 and HT cyt c552-PA cyt c551 chimeric proteins
Keywords keywords	Chimeric protein, 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.

5xed__assembly_1__model_1

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

Download this curve (.dat)

5xed__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5xed__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	20.06 Å
Rg (electron density)	19.29 Å
Total Rg	20.07 Å
Atom count	1294
Residues	162
Excluded volume	23241 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5xed__assembly_1__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 (4)

Entity 1 Entity 1 polymer

Description description	Cytochrome c-551,Cytochrome c-552
Molecular weight formula_weight	8726.0 kDa
Mutation mutation	M61A
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	1361

EDPEVLFKNKGCVACHAIDTKKVGPAYADVAKKYAGRKDAVDYLAGKIKKGGSGVWGSVPAPPQNVTDAEAKQLAQWILSIK

Source Source

Source organism organism	Hydrogenobacter thermophilus
NCBI taxonomy ID ncbi_taxonomy_id	608538
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Cytochrome c-552,Cytochrome c-551
Molecular weight formula_weight	8504.7 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

NEQLAKQKGCMACHDLKAKMVGPAYKDVAAKFAGQAGAEAELAQRIKNGSQGVWGPIPMPPNAVSDDEAQTLAKWVLSQK

Source Source

Source organism organism	Pseudomonas aeruginosa
NCBI taxonomy ID ncbi_taxonomy_id	208964
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 non-polymer

Description description	HEME C
Molecular weight formula_weight	618.5 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	67

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6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d5xeda_
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.3.1.1 — monodomain cytochrome c

Domain ID domain_id	d5xedc_
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.3.1.1 — monodomain cytochrome c

CATH v4.4 (2 domains)

Domain ID domain_id	5xedA01
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

Domain ID domain_id	5xedC01
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

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Unit-cell length a length_a	32.088 Å
Unit-cell length b length_b	65.912 Å
Unit-cell length c length_c	35.380 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	103.72 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	2

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

Resolution resolution	1.550 Å
Low-resolution limit resolution_low	34.370 Å
R factor r_factor	0.2102
R_work r_work	0.2087
R_free r_free	0.2376

Heterodimer constructed from M61A PA cyt c551-HT cyt c552 and HT cyt c552-PA cyt c551 chimeric proteins

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

Cytochrome c-551,Cytochrome c-552

State in the Current Structure

Other States of the Same Protein in the Database

Cytochrome c-551,Cytochrome c-552

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

5xed__assembly_1__model_1

5xed__assembly_1__model_1 | I(q)

5xed__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)

Heterodimer constructed from M61A PA cyt c551-HT cyt c552 and HT cyt c552-PA cyt c551 chimeric proteins

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

Cytochrome c-551,Cytochrome c-552

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Cytochrome c-551,Cytochrome c-552

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

5xed__assembly_1__model_1

5xed__assembly_1__model_1 | I(q)

5xed__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)