2zon

Crystal structure of electron transfer complex of nitrite reductase with cytochrome c

Method: X-RAY DIFFRACTION

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

Dissimilatory copper-containing nitrite reductase

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	cytochrome c551 × 1 COPPER (II) ION × 6 PROTOPORPHYRIN IX CONTAINING FE × 1 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	O68601_ALCXX
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–336； UniProt 25–360 Author chain B； PDBConstruct 1–336； UniProt 25–360 Author chain C； PDBConstruct 1–336； UniProt 25–360

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	2zon
Deposition date deposition_date	2008-05-27
Structure title title	Crystal structure of electron transfer complex of nitrite reductase with cytochrome c
Keywords keywords	nitrite, electron transfer, denitrification, OXIDOREDUCTASE-electron transport COMPLEX; OXIDOREDUCTASE/electron transport
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.

2zon__assembly_1__model_1

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

Download this curve (.dat)

2zon__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2zon__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	29.74 Å
Rg (electron density)	28.91 Å
Total Rg	29.78 Å
Atom count	8291
Residues	1083
Excluded volume	147510 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2zon__assembly_1__model_1`	tetrameric （4）	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	Dissimilatory copper-containing nitrite reductase
Molecular weight formula_weight	36570.5 kDa
EC 编号 ec_number	1.7.2.1
Source method src_method	nat
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C
Atom count atom_count	9364

QDADKLPHTKVTLVAPPQVHPHEQATKSGPKVVEFTMTIEEKKMVIDDKGTTLQAMTFNGSMPGPTLVVHEGDYVQLTLVNPATNAMPHNVDFHGATGALGGAKLTNVNPGEQATLRFKADRSGTFVYHCAPEGMVPWHVVSGMSGTLMVLPRDGLKDPQGKPLHYDRAYTIGEFDLYIPKGPDGKYKDYATLAESYGDTVQVMRTLTPSHIVFNGKVGALTGANALTAKVGETVLLIHSQANRDTRPHLIGGHGDWVWETGKFANPPQRDLETWFIRGGSAGAALYTFKQPGVYAYLNHNLIEAFELGAAGHIKVEGKWNDDLMKQIKAPAPIPR

Entity 2 Entity 2 polymer

Description description	cytochrome c551
Molecular weight formula_weight	8761.0 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	G

AADAPAQLDPAGEKLYRSACVVCHASGVANAPKLGDKQAWAPFLAQGADALLATVLKGKGAMPPRGGTAADEATLRAAVAYMMDAAR

Entity 3 Entity 3 non-polymer

Description description	COPPER (II) ION
Molecular weight formula_weight	63.5 kDa
Source method src_method	syn
Copy count entity_count	6

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	1

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1073

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6. Fold Classification (SCOP + CATH) 14 domains

SCOP 2.08 (7 domains)

Domain ID domain_id	d2zona1
Class class	b — All beta proteins
Fold Fold fold	b.6 — Cupredoxin-like
Superfamily Superfamily superfamily	b.6.1 — Cupredoxins
Family Family family	b.6.1.3 — Multidomain cupredoxins

Domain ID domain_id	d2zona2
Class class	b — All beta proteins
Fold Fold fold	b.6 — Cupredoxin-like
Superfamily Superfamily superfamily	b.6.1 — Cupredoxins
Family Family family	b.6.1.3 — Multidomain cupredoxins

Domain ID domain_id	d2zonb1
Class class	b — All beta proteins
Fold Fold fold	b.6 — Cupredoxin-like
Superfamily Superfamily superfamily	b.6.1 — Cupredoxins
Family Family family	b.6.1.3 — Multidomain cupredoxins

Domain ID domain_id	d2zonb2
Class class	b — All beta proteins
Fold Fold fold	b.6 — Cupredoxin-like
Superfamily Superfamily superfamily	b.6.1 — Cupredoxins
Family Family family	b.6.1.3 — Multidomain cupredoxins

Domain ID domain_id	d2zonc1
Class class	b — All beta proteins
Fold Fold fold	b.6 — Cupredoxin-like
Superfamily Superfamily superfamily	b.6.1 — Cupredoxins
Family Family family	b.6.1.3 — Multidomain cupredoxins

Domain ID domain_id	d2zonc2
Class class	b — All beta proteins
Fold Fold fold	b.6 — Cupredoxin-like
Superfamily Superfamily superfamily	b.6.1 — Cupredoxins
Family Family family	b.6.1.3 — Multidomain cupredoxins

Domain ID domain_id	d2zong_
Class class	a — All alpha proteins
Fold Fold fold	a.3 — Cytochrome c
Superfamily Superfamily superfamily	a.3.1 — Cytochrome c
Family Family family	a.3.1.0 — automated matches

CATH v4.4 (7 domains)

Domain ID domain_id	2zonA01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	420 — Cupredoxins - blue copper proteins

Domain ID domain_id	2zonA02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	420 — Cupredoxins - blue copper proteins

Domain ID domain_id	2zonB01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	420 — Cupredoxins - blue copper proteins

Domain ID domain_id	2zonB02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	420 — Cupredoxins - blue copper proteins

Domain ID domain_id	2zonC01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	420 — Cupredoxins - blue copper proteins

Domain ID domain_id	2zonC02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	420 — Cupredoxins - blue copper proteins

Domain ID domain_id	2zonG00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	760 — Cytochrome Bc1 Complex; Chain D, domain 2
Homologous superfamily homologous superfamily	10 — Cytochrome c-like domain

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Unit-cell length a length_a	63.345 Å
Unit-cell length b length_b	103.942 Å
Unit-cell length c length_c	163.144 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	12

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	1.700 Å
Low-resolution limit resolution_low	8.000 Å
R factor r_factor	0.1655
R_work r_work	0.1622
R_free r_free	0.1954

Crystal structure of electron transfer complex of nitrite reductase with cytochrome c

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

Dissimilatory copper-containing nitrite reductase

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

2zon__assembly_1__model_1

2zon__assembly_1__model_1 | I(q)

2zon__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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 14 domains

SCOP 2.08 (7 domains)

CATH v4.4 (7 domains)

7. Citations (1)

Crystal structure of electron transfer complex of nitrite reductase with cytochrome c

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

Dissimilatory copper-containing nitrite reductase

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

2zon__assembly_1__model_1

2zon__assembly_1__model_1 | I(q)

2zon__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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 14 domains

SCOP 2.08 (7 domains)

CATH v4.4 (7 domains)

7. Citations (1)