SAXSdb — 1vzg

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

DESULFOFERRODOXIN

DESULFOVIBRIO BAARSII

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	FE (III) ION × 4 CALCIUM ION × 1 HEXACYANOFERRATE(3-) × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	DESR_DESBR
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–126； UniProt 1–126 Author chain B； PDBConstruct 1–126； UniProt 1–126

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	1vzg
Deposition date deposition_date	2004-05-19
Structure title title	Structure of superoxide reductase bound to ferrocyanide and active site expansion upon X-ray induced photoreduction
Keywords keywords	FERROCYANIDE, MICROSPECTROPHOTOMETRY, REDOX STATES, PHOTOREDUCTION, DINUCLEAR IRON CLUSTER, OXIDOREDUCTASE, ELECTRON TRANSPORT; OXIDOREDUCTASE
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.

1vzg__assembly_1__model_1

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

Download this curve (.dat)

1vzg__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1vzg__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	19.19 Å
Rg (electron density)	18.02 Å
Total Rg	19.05 Å
Atom count	1987
Residues	250
Excluded volume	35510 Å³
Maximum q	0.500 Å⁻¹

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

Entity 1 Entity 1 polymer

Description description	DESULFOFERRODOXIN
Molecular weight formula_weight	14118.4 kDa
EC 编号 ec_number	1.15.1.2
Mutation mutation	YES
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	2322

MPERLQVYKCEVCGNIVEVLNGGIGELVCCNQDMKLMSENTVDAAKAKHVPVIEKIDGGYKVKVGAVAHPMEEKHYIQWIELLADDKCYTQFLKPGQAPEAVFLIEAAKVVAREYCNIHGHWKAEN

Source Source

Source organism organism	DESULFOVIBRIO BAARSII
Common name common_name	DESULFOARCULUS BAARSII
NCBI taxonomy ID ncbi_taxonomy_id	887
Host organism host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 non-polymer

Description description	FE (III) ION
Molecular weight formula_weight	55.8 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	HEXACYANOFERRATE(3-)
Molecular weight formula_weight	211.9 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	161

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6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1vzga1
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.13 — Superoxide reductase-like
Family Family family	b.1.13.1 — Superoxide reductase-like

Domain ID domain_id	d1vzga2
Class class	g — Small proteins
Fold Fold fold	g.41 — Rubredoxin-like
Superfamily Superfamily superfamily	g.41.5 — Rubredoxin-like
Family Family family	g.41.5.2 — Desulforedoxin

Domain ID domain_id	d1vzgb1
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.13 — Superoxide reductase-like
Family Family family	b.1.13.1 — Superoxide reductase-like

Domain ID domain_id	d1vzgb2
Class class	g — Small proteins
Fold Fold fold	g.41 — Rubredoxin-like
Superfamily Superfamily superfamily	g.41.5 — Rubredoxin-like
Family Family family	g.41.5.2 — Desulforedoxin

CATH v4.4 (4 domains)

Domain ID domain_id	1vzgA01
Class class	2 — Mainly Beta
Architecture architecture	20 — Single Sheet
Topology topology	28 — Rubrerythrin, domain 2
Homologous superfamily homologous superfamily	100 — Desulphoferrodoxin, N-terminal domain

Domain ID domain_id	1vzgA02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	730 — SOR catalytic domain

Domain ID domain_id	1vzgB01
Class class	2 — Mainly Beta
Architecture architecture	20 — Single Sheet
Topology topology	28 — Rubrerythrin, domain 2
Homologous superfamily homologous superfamily	100 — Desulphoferrodoxin, N-terminal domain

Domain ID domain_id	1vzgB02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	730 — SOR catalytic domain

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Unit-cell length a length_a	42.130 Å
Unit-cell length b length_b	67.650 Å
Unit-cell length c length_c	82.190 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	8

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

Resolution resolution	1.690 Å
Low-resolution limit resolution_low	37.490 Å
R factor r_factor	0.2050
R_work r_work	0.2050
R_free r_free	0.2490

Structure of superoxide reductase bound to ferrocyanide and active site expansion upon X-ray induced photoreduction

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

DESULFOFERRODOXIN

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

1vzg__assembly_1__model_1

1vzg__assembly_1__model_1 | I(q)

1vzg__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 (5)

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 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)

Structure of superoxide reductase bound to ferrocyanide and active site expansion upon X-ray induced photoreduction

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

DESULFOFERRODOXIN

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

1vzg__assembly_1__model_1

1vzg__assembly_1__model_1 | I(q)

1vzg__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 (5)

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 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)