2dvh

THE Y64A MUTANT OF CYTOCHROME C553 FROM DESULFOVIBRIO VULGARIS HILDENBOROUGH, NMR, 39 STRUCTURES

Method: SOLUTION NMR

▼

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

CYTOCHROME C-553

Desulfovibrio vulgaris subsp. vulgaris str. Hildenborough

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 × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CY553_DESVH
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–79； UniProt 25–103

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	2dvh
Deposition date deposition_date	1998-03-25
Structure title title	THE Y64A MUTANT OF CYTOCHROME C553 FROM DESULFOVIBRIO VULGARIS HILDENBOROUGH, NMR, 39 STRUCTURES
Keywords keywords	ELECTRON TRANSPORT, CYTOCHROME C, HEME; ELECTRON TRANSPORT
Experimental Method method	SOLUTION NMR

▼

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.

2dvh__assembly_1__model_32

Assembly 1 · Model 32 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

2dvh__assembly_1__model_32 | I(q)

100 plotted points; both axes use logarithmic scales.

2dvh__assembly_1__model_32 | P(r) · Pending

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

Rg（Guinier）	12.46 Å
Rg (electron density)	11.07 Å
Total Rg	12.45 Å
Atom count	1216
Residues	79
Excluded volume	10962 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2dvh__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	2	`2dvh__assembly_1__model_2`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	3	`2dvh__assembly_1__model_3`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	4	`2dvh__assembly_1__model_4`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	5	`2dvh__assembly_1__model_5`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	6	`2dvh__assembly_1__model_6`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	7	`2dvh__assembly_1__model_7`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	8	`2dvh__assembly_1__model_8`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	9	`2dvh__assembly_1__model_9`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	10	`2dvh__assembly_1__model_10`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	11	`2dvh__assembly_1__model_11`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	12	`2dvh__assembly_1__model_12`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	13	`2dvh__assembly_1__model_13`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	14	`2dvh__assembly_1__model_14`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	15	`2dvh__assembly_1__model_15`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	16	`2dvh__assembly_1__model_16`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	17	`2dvh__assembly_1__model_17`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	18	`2dvh__assembly_1__model_18`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	19	`2dvh__assembly_1__model_19`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	20	`2dvh__assembly_1__model_20`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	21	`2dvh__assembly_1__model_21`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	22	`2dvh__assembly_1__model_22`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	23	`2dvh__assembly_1__model_23`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	24	`2dvh__assembly_1__model_24`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	25	`2dvh__assembly_1__model_25`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	26	`2dvh__assembly_1__model_26`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	27	`2dvh__assembly_1__model_27`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	28	`2dvh__assembly_1__model_28`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	29	`2dvh__assembly_1__model_29`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	30	`2dvh__assembly_1__model_30`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	31	`2dvh__assembly_1__model_31`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	32	`2dvh__assembly_1__model_32`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	33	`2dvh__assembly_1__model_33`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	34	`2dvh__assembly_1__model_34`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	35	`2dvh__assembly_1__model_35`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	36	`2dvh__assembly_1__model_36`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	37	`2dvh__assembly_1__model_37`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	38	`2dvh__assembly_1__model_38`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	39	`2dvh__assembly_1__model_39`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (2)

▼

6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d2dvha_
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 (1 domains)

Domain ID domain_id	2dvhA00
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	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 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	1

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

Description description	CYTOCHROME C-553
Molecular weight formula_weight	8225.4 kDa
Mutation mutation	Y64A
Source method src_method	man
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	47424

Source organism organism	Desulfovibrio vulgaris subsp. vulgaris str. Hildenborough
NCBI taxonomy ID ncbi_taxonomy_id	882
Host organism host_organism	Desulfovibrio desulfuricans

THE Y64A MUTANT OF CYTOCHROME C553 FROM DESULFOVIBRIO VULGARIS HILDENBOROUGH, NMR, 39 STRUCTURES

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

CYTOCHROME C-553

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

2dvh__assembly_1__model_32

2dvh__assembly_1__model_32 | I(q)

2dvh__assembly_1__model_32 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

5. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

7. Citations (1)

Description description	HEME C
Molecular weight formula_weight	618.5 kDa
Source method src_method	syn
Copy count entity_count	1

THE Y64A MUTANT OF CYTOCHROME C553 FROM DESULFOVIBRIO VULGARIS HILDENBOROUGH, NMR, 39 STRUCTURES

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

CYTOCHROME C-553

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

2dvh__assembly_1__model_32

2dvh__assembly_1__model_32 | I(q)

2dvh__assembly_1__model_32 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

5. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

7. Citations (1)