1t6u

Nickel Superoxide Dismutase (NiSOD) Native 1.30 A Structure

Method: X-RAY DIFFRACTION

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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	NICKEL (II) ION × 6 water × 6	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 6	NICKEL (II) ION × 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 Author chain D； PDBConstruct 1–117； UniProt 15–131 Author chain E； PDBConstruct 1–117； UniProt 15–131 Author chain F； PDBConstruct 1–117； UniProt 15–131 Author chain G； PDBConstruct 1–117； UniProt 15–131 Author chain H； PDBConstruct 1–117； UniProt 15–131 Author chain I； PDBConstruct 1–117； UniProt 15–131 Author chain J； PDBConstruct 1–117； UniProt 15–131 Author chain K； PDBConstruct 1–117； UniProt 15–131 Author chain L； 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	1t6u
Deposition date deposition_date	2004-05-07
Structure title title	Nickel Superoxide Dismutase (NiSOD) Native 1.30 A Structure
Keywords keywords	Nickel, 4-helix bundle, hexamer, superoxide dismutase, NiSOD, SOD, high resolution, 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.

1t6u__assembly_2__model_1

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

Download this curve (.dat)

1t6u__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1t6u__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	25.61 Å
Rg (electron density)	24.82 Å
Total Rg	25.52 Å
Atom count	5580
Residues	699
Excluded volume	98990 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1t6u__assembly_1__model_1`	hexameric （6）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1t6u__assembly_2__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 (3)

Entity 1 Entity 1 polymer

Description description	Superoxide dismutase [Ni]
Molecular weight formula_weight	13241.0 kDa
EC 编号 ec_number	1.15.1.1
Mutation mutation	L85M
Source method src_method	man
Copy count entity_count	12

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G,H,I,J,K,L
Atom count atom_count	13192

HCDLPCGVYDPAQARIEAESVKAVQEKMAGNDDPHFQTRATVIKEQRAELAKHHVSVLWSDYFKPPHFEKYPELHQLVNDTLKAMSAAKGSKDPATGQKALDYIAQIDKIFWETKKA

Source Source

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

Entity 2 Entity 2 non-polymer

Description description	NICKEL (II) ION
Molecular weight formula_weight	58.7 kDa
Source method src_method	syn
Copy count entity_count	12

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1926

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6. Fold Classification (SCOP + CATH) 24 domains

SCOP 2.08 (12 domains)

Domain ID domain_id	d1t6ua_
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	d1t6ub_
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	d1t6uc_
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	d1t6ud_
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	d1t6ue_
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	d1t6uf_
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	d1t6ug_
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	d1t6uh_
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	d1t6ui_
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	d1t6uj_
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	d1t6uk_
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	d1t6ul_
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 (12 domains)

Domain ID domain_id	1t6uA00
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	1t6uB00
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	1t6uC00
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	1t6uD00
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	1t6uE00
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	1t6uF00
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	1t6uG00
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	1t6uH00
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	1t6uI00
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	1t6uJ00
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	1t6uK00
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	1t6uL00
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	64.147 Å
Unit-cell length b length_b	111.680 Å
Unit-cell length c length_c	106.834 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	94.51 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	24

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

Resolution resolution	1.300 Å
Low-resolution limit resolution_low	50.000 Å
R factor r_factor	—
R_work r_work	0.1579
R_free r_free	0.2014

Nickel Superoxide Dismutase (NiSOD) Native 1.30 A Structure

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

1t6u__assembly_2__model_1

1t6u__assembly_2__model_1 | I(q)

1t6u__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 24 domains

SCOP 2.08 (12 domains)

CATH v4.4 (12 domains)

7. Citations (1)

Nickel Superoxide Dismutase (NiSOD) Native 1.30 A Structure

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

1t6u__assembly_2__model_1

1t6u__assembly_2__model_1 | I(q)

1t6u__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 24 domains

SCOP 2.08 (12 domains)

CATH v4.4 (12 domains)

7. Citations (1)