2ji2

X-ray structure of E114A mutant of superoxide reductase from Desulfoarculus baarsii in the native, reduced form

Method: X-RAY DIFFRACTION

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

Desulfoferrodoxin

Desulfarculus 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 × 2 NITRATE ION × 2 FE (II) ION × 2 CALCIUM ION × 1 water × 2	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	FE (III) ION × 2 NITRATE ION × 2 FE (II) ION × 2 CALCIUM ION × 3 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	DFX_DESB2
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 Author chain C； PDBConstruct 1–126； UniProt 1–126 Author chain D； 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	2ji2
Deposition date deposition_date	2007-02-24
Structure title title	X-ray structure of E114A mutant of superoxide reductase from Desulfoarculus baarsii in the native, reduced form
Keywords keywords	;OXIDOREDUCTASE, RAMAN SPECTROSCOPY, SUPEROXIDE REDUCTASE, INTERMEDIATE TRAPPING, MICROSPECTROPHOTOMETRY, DETOXIFICATION, ELECTRON TRANSPORT, IRON, TRANSPORT, REDOX STATES, METAL-BINDING ;; 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.

2ji2__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

2ji2__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2ji2__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	19.00 Å
Rg (electron density)	17.91 Å
Total Rg	18.91 Å
Atom count	1950
Residues	251
Excluded volume	34943 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2ji2__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2ji2__assembly_2__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 (6)

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	E114A
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	4534

MPERLQVYKCEVCGNIVEVLNGGIGELVCCNQDMKLMSENTVDAAKEKHVPVIEKIDGGYKVKVGAVAHPMEEKHYIQWIELLADDKCYTQFLKPGQAPEAVFLIEAAKVVARAYCNIHGHWKAEN

Source Source

Source organism organism	Desulfarculus baarsii
NCBI taxonomy ID ncbi_taxonomy_id	453230
Host organism host_organism	Escherichia coli DH5[alpha]

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	NITRATE ION
Molecular weight formula_weight	62.0 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 non-polymer

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

Entity 5 Entity 5 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	568

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6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d2ji2a1
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	d2ji2a2
Class class	g — Small proteins
Fold Fold fold	g.41 — Rubredoxin-like
Superfamily Superfamily superfamily	g.41.5 — Rubredoxin-like
Family Family family	g.41.5.0 — automated matches

Domain ID domain_id	d2ji2b1
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	d2ji2b2
Class class	g — Small proteins
Fold Fold fold	g.41 — Rubredoxin-like
Superfamily Superfamily superfamily	g.41.5 — Rubredoxin-like
Family Family family	g.41.5.0 — automated matches

Domain ID domain_id	d2ji2c1
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	d2ji2c2
Class class	g — Small proteins
Fold Fold fold	g.41 — Rubredoxin-like
Superfamily Superfamily superfamily	g.41.5 — Rubredoxin-like
Family Family family	g.41.5.0 — automated matches

Domain ID domain_id	d2ji2d1
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	d2ji2d2
Class class	g — Small proteins
Fold Fold fold	g.41 — Rubredoxin-like
Superfamily Superfamily superfamily	g.41.5 — Rubredoxin-like
Family Family family	g.41.5.0 — automated matches

CATH v4.4 (8 domains)

Domain ID domain_id	2ji2A01
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	2ji2A02
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	2ji2B01
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	2ji2B02
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	2ji2C01
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	2ji2C02
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	2ji2D01
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	2ji2D02
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	70.470 Å
Unit-cell length b length_b	82.870 Å
Unit-cell length c length_c	201.950 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	32

Space group space_group	I 2 2 2
Space-group number int_tables_number	23
Crystal system crystal_system	—

Resolution resolution	1.700 Å
Low-resolution limit resolution_low	47.400 Å
R factor r_factor	0.1950
R_work r_work	0.1950
R_free r_free	0.2220

X-ray structure of E114A mutant of superoxide reductase from Desulfoarculus baarsii in the native, reduced form

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

2ji2__assembly_2__model_1

2ji2__assembly_2__model_1 | I(q)

2ji2__assembly_2__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 (6)

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 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

CATH v4.4 (8 domains)

7. Citations (1)

X-ray structure of E114A mutant of superoxide reductase from Desulfoarculus baarsii in the native, reduced form

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

2ji2__assembly_2__model_1

2ji2__assembly_2__model_1 | I(q)

2ji2__assembly_2__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 (6)

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 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

CATH v4.4 (8 domains)

7. Citations (1)