SAXSdb — 4ncq

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

Superoxide dismutase [Ni]

Streptomyces coelicolor

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 6	water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SODN_STRCO
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–117； UniProt 15–131 Author chain B； PDBConstruct 1–117； UniProt 15–131 Author chain C； PDBConstruct 1–117； UniProt 15–131

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	4ncq
Deposition date deposition_date	2013-10-24
Structure title title	Crystal structure of NiSOD H1A mutant
Keywords keywords	antioxidant, hexamer, superoxide dismutase, NiSOD, SOD, oxidoreductase, metal-binding, Ni-binding, Ni; 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.

4ncq__assembly_1__model_1

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

Download this curve (.dat)

4ncq__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4ncq__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	25.88 Å
Rg (electron density)	24.92 Å
Total Rg	25.75 Å
Atom count	5294
Residues	660
Excluded volume	94049 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4ncq__assembly_1__model_1`	hexameric （6）	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 (2)

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6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d4ncqa_
Class class	a — All alpha proteins
Fold Fold fold	a.24 — Four-helical up-and-down bundle
Superfamily Superfamily superfamily	a.24.22 — Nickel-containing superoxide dismutase, NiSOD
Family Family family	a.24.22.1 — Nickel-containing superoxide dismutase, NiSOD

Domain ID domain_id	d4ncqb_
Class class	a — All alpha proteins
Fold Fold fold	a.24 — Four-helical up-and-down bundle
Superfamily Superfamily superfamily	a.24.22 — Nickel-containing superoxide dismutase, NiSOD
Family Family family	a.24.22.1 — Nickel-containing superoxide dismutase, NiSOD

Domain ID domain_id	d4ncqc_
Class class	a — All alpha proteins
Fold Fold fold	a.24 — Four-helical up-and-down bundle
Superfamily Superfamily superfamily	a.24.22 — Nickel-containing superoxide dismutase, NiSOD
Family Family family	a.24.22.1 — Nickel-containing superoxide dismutase, NiSOD

CATH v4.4 (3 domains)

Domain ID domain_id	4ncqA00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily	400 — Nickel-containing superoxide dismutase

Domain ID domain_id	4ncqB00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily	400 — Nickel-containing superoxide dismutase

Domain ID domain_id	4ncqC00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily	400 — Nickel-containing superoxide dismutase

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Unit-cell length a length_a	59.950 Å
Unit-cell length b length_b	110.742 Å
Unit-cell length c length_c	111.861 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	24

Space group space_group	C 2 2 21
Space-group number int_tables_number	20
Crystal system crystal_system	—

Resolution resolution	2.080 Å
Low-resolution limit resolution_low	30.930 Å
R factor r_factor	0.1871
R_work r_work	0.1847
R_free r_free	0.2375

Description description	Superoxide dismutase [Ni]
Molecular weight formula_weight	13155.9 kDa
EC 编号 ec_number	1.15.1.1
Mutation mutation	H1A
Source method src_method	man
Copy count entity_count	3

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C
Atom count atom_count	2827

Crystal structure of NiSOD H1A mutant

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

Superoxide dismutase [Ni]

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

4ncq__assembly_1__model_1

4ncq__assembly_1__model_1 | I(q)

4ncq__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 water

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

CATH v4.4 (3 domains)

7. Citations (1)

Source organism organism	Streptomyces coelicolor
NCBI taxonomy ID ncbi_taxonomy_id	1902
Host organism host_organism	Escherichia coli

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	180

Crystal structure of NiSOD H1A mutant

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

Superoxide dismutase [Ni]

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

4ncq__assembly_1__model_1

4ncq__assembly_1__model_1 | I(q)

4ncq__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 water

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

CATH v4.4 (3 domains)

7. Citations (1)