SAXSdb — 1z9n

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

Superoxide dismutase [Cu-Zn]

Haemophilus ducreyi

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	COPPER (II) ION × 2 ZINC ION × 2 PROTOPORPHYRIN IX CONTAINING FE × 1 water × 2	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	COPPER (II) ION × 2 ZINC ION × 2 PROTOPORPHYRIN IX CONTAINING FE × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SODC_HAEDU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–177； UniProt 23–199 Author chain B； PDBConstruct 1–177； UniProt 23–199 Author chain C； PDBConstruct 1–177； UniProt 23–199 Author chain D； PDBConstruct 1–177； UniProt 23–199

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	1z9n
Deposition date deposition_date	2005-04-03
Structure title title	X-Ray structure of a Cu-Zn superoxide dismutase from Haemophilus ducreyi with haem bound at the dimer interface
Keywords keywords	CU-ZN SOD; SOD; HAEM, 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.

1z9n__assembly_2__model_1

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

Download this curve (.dat)

1z9n__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1z9n__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	20.93 Å
Rg (electron density)	19.95 Å
Total Rg	20.91 Å
Atom count	2369
Residues	310
Excluded volume	41895 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1z9n__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1z9n__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 (5)

Entity 1 Entity 1 polymer

Description description	Superoxide dismutase [Cu-Zn]
Molecular weight formula_weight	19120.8 kDa
EC 编号 ec_number	1.15.1.1
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	5854

HGDHMHNHDTKMDTMSKDMMSMEKIVVPVQQLDPQNGNKDVGTVEITESAYGLVFTPKLHDLAHGLHGFHIHEKPSCEPKEKDGKLVAGLGAGGHWDPKQTQKHGYPWSDDAHMGDLPALFVMHDGSATTPVLAPRLKKLAEVKGHSLMIHAGGDNHSDHPAPLGGGGPRMACGVIK

Source Source

Source organism organism	Haemophilus ducreyi
NCBI taxonomy ID ncbi_taxonomy_id	730
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	COPPER (II) ION
Molecular weight formula_weight	63.5 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 non-polymer

Description description	PROTOPORPHYRIN IX CONTAINING FE
Molecular weight formula_weight	616.5 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	1082

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6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1z9na_
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.8 — Cu,Zn superoxide dismutase-like
Family Family family	b.1.8.1 — Cu,Zn superoxide dismutase-like

Domain ID domain_id	d1z9nb_
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.8 — Cu,Zn superoxide dismutase-like
Family Family family	b.1.8.1 — Cu,Zn superoxide dismutase-like

Domain ID domain_id	d1z9nc_
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.8 — Cu,Zn superoxide dismutase-like
Family Family family	b.1.8.1 — Cu,Zn superoxide dismutase-like

Domain ID domain_id	d1z9nd_
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.8 — Cu,Zn superoxide dismutase-like
Family Family family	b.1.8.1 — Cu,Zn superoxide dismutase-like

CATH v4.4 (4 domains)

Domain ID domain_id	1z9nA00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	200 — Superoxide dismutase, copper/zinc binding domain

Domain ID domain_id	1z9nB00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	200 — Superoxide dismutase, copper/zinc binding domain

Domain ID domain_id	1z9nC00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	200 — Superoxide dismutase, copper/zinc binding domain

Domain ID domain_id	1z9nD00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	200 — Superoxide dismutase, copper/zinc binding domain

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Unit-cell length a length_a	37.320 Å
Unit-cell length b length_b	65.900 Å
Unit-cell length c length_c	69.540 Å
Unit-cell angle α angle_alpha	66.59 °
Unit-cell angle β angle_beta	89.87 °
Unit-cell angle γ angle_gamma	76.03 °
Molecules per unit cell Z z_pdb	4

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

Resolution resolution	1.500 Å
Low-resolution limit resolution_low	19.500 Å
R factor r_factor	0.1583
R_work r_work	0.1565
R_free r_free	0.1933

X-Ray structure of a Cu-Zn superoxide dismutase from Haemophilus ducreyi with haem bound at the dimer interface

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

Superoxide dismutase [Cu-Zn]

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

1z9n__assembly_2__model_1

1z9n__assembly_2__model_1 | I(q)

1z9n__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 (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)

X-Ray structure of a Cu-Zn superoxide dismutase from Haemophilus ducreyi with haem bound at the dimer interface

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

Superoxide dismutase [Cu-Zn]

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

1z9n__assembly_2__model_1

1z9n__assembly_2__model_1 | I(q)

1z9n__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 (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)