SAXSdb — 2nyb

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

Superoxide dismutase [FE]

Escherichia coli

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	FE (II) ION × 2 OXYGEN ATOM × 2 water × 2	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	FE (II) ION × 2 OXYGEN ATOM × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SODF_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–192； UniProt 1–192 Author chain B； PDBConstruct 1–192； UniProt 1–192 Author chain C； PDBConstruct 1–192； UniProt 1–192 Author chain D； PDBConstruct 1–192； UniProt 1–192

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	2nyb
Deposition date deposition_date	2006-11-20
Structure title title	Crystal structure of E.Coli Iron Superoxide Dismutase Q69E at 1.1 Angstrom resolution
Keywords keywords	Iron Superoxide Dismutase Q69E, FeSOD, OXIDOREDUCTASE; 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.

2nyb__assembly_2__model_1

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

Download this curve (.dat)

2nyb__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2nyb__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	22.70 Å
Rg (electron density)	21.90 Å
Total Rg	22.89 Å
Atom count	3010
Residues	384
Excluded volume	53161 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2nyb__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2nyb__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 (4)

Entity 1 Entity 1 polymer

Description description	Superoxide dismutase [FE]
Molecular weight formula_weight	21155.5 kDa
EC 编号 ec_number	1.15.1.1
Mutation mutation	Q69E
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	7813

SFELPALPYAKDALAPHISAETIEYHYGKHHQTYVTNLNNLIKGTAFEGKSLEEIIRSSEGGVFNNAAEVWNHTFYWNCLAPNAGGEPTGKVAEAIAASFGSFADFKAQFTDAAIKNFGSGWTWLVKNSDGKLAIVSTSNAGTPLTTDATPLLTVDVWEHAYYIDYRNARPGYLEHFWALVNWEFVAKNLAA

Source Source

Source organism organism	Escherichia coli
NCBI taxonomy ID ncbi_taxonomy_id	562
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 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 3 Entity 3 non-polymer

Description description	OXYGEN ATOM
Molecular weight formula_weight	16.0 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1144

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6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d2nyba1
Class class	a — All alpha proteins
Fold Fold fold	a.2 — Long alpha-hairpin
Superfamily Superfamily superfamily	a.2.11 — Fe,Mn superoxide dismutase (SOD), N-terminal domain
Family Family family	a.2.11.1 — Fe,Mn superoxide dismutase (SOD), N-terminal domain

Domain ID domain_id	d2nyba2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.44 — Fe,Mn superoxide dismutase (SOD), C-terminal domain
Superfamily Superfamily superfamily	d.44.1 — Fe,Mn superoxide dismutase (SOD), C-terminal domain
Family Family family	d.44.1.1 — Fe,Mn superoxide dismutase (SOD), C-terminal domain

Domain ID domain_id	d2nybb1
Class class	a — All alpha proteins
Fold Fold fold	a.2 — Long alpha-hairpin
Superfamily Superfamily superfamily	a.2.11 — Fe,Mn superoxide dismutase (SOD), N-terminal domain
Family Family family	a.2.11.1 — Fe,Mn superoxide dismutase (SOD), N-terminal domain

Domain ID domain_id	d2nybb2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.44 — Fe,Mn superoxide dismutase (SOD), C-terminal domain
Superfamily Superfamily superfamily	d.44.1 — Fe,Mn superoxide dismutase (SOD), C-terminal domain
Family Family family	d.44.1.1 — Fe,Mn superoxide dismutase (SOD), C-terminal domain

Domain ID domain_id	d2nybc1
Class class	a — All alpha proteins
Fold Fold fold	a.2 — Long alpha-hairpin
Superfamily Superfamily superfamily	a.2.11 — Fe,Mn superoxide dismutase (SOD), N-terminal domain
Family Family family	a.2.11.1 — Fe,Mn superoxide dismutase (SOD), N-terminal domain

Domain ID domain_id	d2nybc2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.44 — Fe,Mn superoxide dismutase (SOD), C-terminal domain
Superfamily Superfamily superfamily	d.44.1 — Fe,Mn superoxide dismutase (SOD), C-terminal domain
Family Family family	d.44.1.1 — Fe,Mn superoxide dismutase (SOD), C-terminal domain

Domain ID domain_id	d2nybd1
Class class	a — All alpha proteins
Fold Fold fold	a.2 — Long alpha-hairpin
Superfamily Superfamily superfamily	a.2.11 — Fe,Mn superoxide dismutase (SOD), N-terminal domain
Family Family family	a.2.11.1 — Fe,Mn superoxide dismutase (SOD), N-terminal domain

Domain ID domain_id	d2nybd2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.44 — Fe,Mn superoxide dismutase (SOD), C-terminal domain
Superfamily Superfamily superfamily	d.44.1 — Fe,Mn superoxide dismutase (SOD), C-terminal domain
Family Family family	d.44.1.1 — Fe,Mn superoxide dismutase (SOD), C-terminal domain

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Unit-cell length a length_a	43.508 Å
Unit-cell length b length_b	107.596 Å
Unit-cell length c length_c	84.120 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	94.89 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

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

Resolution resolution	1.100 Å
Low-resolution limit resolution_low	30.290 Å
R factor r_factor	0.1600
R_work r_work	0.1600
R_free r_free	0.1740

Crystal structure of E.Coli Iron Superoxide Dismutase Q69E at 1.1 Angstrom resolution

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

Superoxide dismutase [FE]

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

2nyb__assembly_2__model_1

2nyb__assembly_2__model_1 | I(q)

2nyb__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 (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) 8 domains

SCOP 2.08 (8 domains)

7. Citations (1)

Crystal structure of E.Coli Iron Superoxide Dismutase Q69E at 1.1 Angstrom resolution

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

Superoxide dismutase [FE]

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

2nyb__assembly_2__model_1

2nyb__assembly_2__model_1 | I(q)

2nyb__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 (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) 8 domains

SCOP 2.08 (8 domains)

7. Citations (1)