4ax3

Structure of three-domain heme-Cu nitrite reductase from Ralstonia pickettii at 1.6 A resolution

Method: X-RAY DIFFRACTION

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

COPPER-CONTAINING NITRITE REDUCTASE

RALSTONIA PICKETTII

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 3	COPPER (II) ION × 6 HEME C × 3 water × 3	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 3	COPPER (II) ION × 6 HEME C × 3 water × 3	Consistent with protein count
3	Protein homooligomer	Homooligomer	Protein 3	COPPER (II) ION × 6 HEME C × 3 water × 3	Consistent with protein count
4	Protein homooligomer	Homooligomer	Protein 3	COPPER (II) ION × 6 HEME C × 3 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	E2STD2_9RALS
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–468； UniProt 32–499 Author chain B； PDBConstruct 1–468； UniProt 32–499 Author chain C； PDBConstruct 1–468； UniProt 32–499 Author chain D； PDBConstruct 1–468； UniProt 32–499

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	4ax3
Deposition date deposition_date	2012-06-07
Structure title title	Structure of three-domain heme-Cu nitrite reductase from Ralstonia pickettii at 1.6 A resolution
Keywords keywords	THREE-DOMAIN HEME-CU NITRITE REDUCTASE, ELECTRON TRANSFER, OXIDOREDUCTASE, PROTON CHANNEL, DENITRIFICATION; 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.

4ax3__assembly_1__model_1

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

Download this curve (.dat)

4ax3__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4ax3__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	32.59 Å
Rg (electron density)	31.50 Å
Total Rg	32.22 Å
Atom count	10419
Residues	1365
Excluded volume	185400 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4ax3__assembly_1__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`4ax3__assembly_2__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`4ax3__assembly_3__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`4ax3__assembly_4__model_1`	trimeric （3）	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	COPPER-CONTAINING NITRITE REDUCTASE
Molecular weight formula_weight	49948.5 kDa
EC 编号 ec_number	1.7.2.1
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	16795

ASAKLPGDFGPPRGEPIHAVLTSPPLVPPPVNRTYPAKVIVELEVVEKEMQISEGVSYTFWTFGGTVPGSFIRVRQGDTVEFHLKNHPSSKMPHNIDLHGVTGPGGGAASSFTAPGHESQFTFKALNEGIYVYHCATAPVGMHIANGMYGLILVEPPEGLPKVDHEYYVMQGDFYTAGKYREKGLQPFDMEKAIDERPSYVLFNGAEGALTGDKALHAKVGETVRIFVGNGGPNLVSSFHVIGAIFDQVRYEGGTNVQKNVQTTLIPAGGAAVVKFTARVPGSYVLVDHSIFRAFNKGAMAILKIDGAENKLVYSGKELDSVYLGDRAAPNMSAVTKATQASVSGTLTVQDQVQAGRALFAGTCSVCHQGNGAGLPGVFPPLAKSDFLAADPKRAMNIVLHGLNGKIKVNGQEYDSVMPPMTQLNDDEVANILTYVLNSWDNPGGRVSAEDVKKVRAQPAPAKAVAEH

Source Source

Source organism organism	RALSTONIA PICKETTII
NCBI taxonomy ID ncbi_taxonomy_id	402626
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	8

Entity 3 Entity 3 non-polymer

Description description	HEME C
Molecular weight formula_weight	618.5 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	2470

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6. Fold Classification (SCOP + CATH) 12 domains

CATH v4.4 (12 domains)

Domain ID domain_id	4ax3A01
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	4ax3A02
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	4ax3A03
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

Domain ID domain_id	4ax3B01
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	4ax3B02
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	4ax3B03
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

Domain ID domain_id	4ax3C01
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	4ax3C02
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	4ax3C03
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

Domain ID domain_id	4ax3D01
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	4ax3D02
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	4ax3D03
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	185.812 Å
Unit-cell length b length_b	185.812 Å
Unit-cell length c length_c	185.812 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	48

Space group space_group	P 21 3
Space-group number int_tables_number	198
Crystal system crystal_system	—

Resolution resolution	1.600 Å
Low-resolution limit resolution_low	25.000 Å
R factor r_factor	0.1645
R_work r_work	0.1630
R_free r_free	0.1941

Structure of three-domain heme-Cu nitrite reductase from Ralstonia pickettii at 1.6 A resolution

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

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

4ax3__assembly_1__model_1

4ax3__assembly_1__model_1 | I(q)

4ax3__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 (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) 12 domains

CATH v4.4 (12 domains)

7. Citations (1)

Structure of three-domain heme-Cu nitrite reductase from Ralstonia pickettii at 1.6 A resolution

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

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

4ax3__assembly_1__model_1

4ax3__assembly_1__model_1 | I(q)

4ax3__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 (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) 12 domains

CATH v4.4 (12 domains)

7. Citations (1)