SAXSdb — 1wr5

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

Cytochrome c3

;Desulfovibrio vulgaris str. 'Miyazaki F' ;

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	HEME C × 4 ETHANOL × 14 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CYC3_DESVM
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–108； UniProt 23–130

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	1wr5
Deposition date deposition_date	2004-10-11
Structure title title	Three dimensional Structure of the E41K mutant of Tetraheme Cytochrome c3 from Desulfovibrio vulgaris Miyazaki F
Keywords keywords	tetraheme cytochrome c3, high resolution X-ray structure, E41K mutant, 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.

1wr5__assembly_1__model_1

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

Download this curve (.dat)

1wr5__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1wr5__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	14.46 Å
Rg (electron density)	13.55 Å
Total Rg	14.92 Å
Atom count	1020
Residues	108
Excluded volume	18477 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1wr5__assembly_1__model_1`	monomeric （1）	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 c3
Molecular weight formula_weight	11629.4 kDa
Mutation mutation	E41K
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	1264

AAPKAPADGLKMDKTKQPVVFNHSTHKAVKCGDCHHPVNGKKDYQKCATAGCHDNMDKKDKSAKGYYHAMHDKGTKFKSCVGCHLETAGADAAKKKELTGCKGSKCHS

Source Source

Source organism organism	;Desulfovibrio vulgaris str. 'Miyazaki F' ;
NCBI taxonomy ID ncbi_taxonomy_id	883
Host organism host_organism	Shewanella oneidensis

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 non-polymer

Description description	ETHANOL
Molecular weight formula_weight	46.1 kDa
Source method src_method	syn
Copy count entity_count	14

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	244

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6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1wr5a_
Class class	a — All alpha proteins
Fold Fold fold	a.138 — Multiheme cytochromes
Superfamily Superfamily superfamily	a.138.1 — Multiheme cytochromes
Family Family family	a.138.1.1 — Cytochrome c3-like

CATH v4.4 (1 domains)

Domain ID domain_id	1wr5A00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	10 — Cytochrome C3
Homologous superfamily homologous superfamily	10 — Cytochrome C3

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Unit-cell length a length_a	52.118 Å
Unit-cell length b length_b	67.511 Å
Unit-cell length c length_c	34.142 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	1.400 Å
Low-resolution limit resolution_low	10.000 Å
R factor r_factor	0.1380
R_work r_work	0.1340
R_free r_free	0.2250

Three dimensional Structure of the E41K mutant of Tetraheme Cytochrome c3 from Desulfovibrio vulgaris Miyazaki F

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

Cytochrome c3

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

1wr5__assembly_1__model_1

1wr5__assembly_1__model_1 | I(q)

1wr5__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 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

7. Citations (1)

Three dimensional Structure of the E41K mutant of Tetraheme Cytochrome c3 from Desulfovibrio vulgaris Miyazaki F

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

Cytochrome c3

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

1wr5__assembly_1__model_1

1wr5__assembly_1__model_1 | I(q)

1wr5__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 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

7. Citations (1)