SAXSdb — 2yqb

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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

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

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	2yqb
Deposition date deposition_date	2012-11-07
Structure title title	Structure of P93A variant of three-domain heme-Cu nitrite reductase from Ralstonia pickettii at 1.4 A resolution
Keywords keywords	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.

2yqb__assembly_1__model_1

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

Download this curve (.dat)

2yqb__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2yqb__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	32.51 Å
Rg (electron density)	31.44 Å
Total Rg	32.15 Å
Atom count	10386
Residues	1362
Excluded volume	184830 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2yqb__assembly_1__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	49922.5 kDa
EC 编号 ec_number	1.7.2.1
Mutation mutation	YES
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	4549

ASAKLPGDFGPPRGEPIHAVLTSPPLVPPPVNRTYPAKVIVELEVVEKEMQISEGVSYTFWTFGGTVPGSFIRVRQGDTVEFHLKNHPSSKMAHNIDLHGVTGPGGGAASSFTAPGHESQFTFKALNEGIYVYHCATAPVGMHIANGMYGLILVEPPEGLPKVDHEYYVMQGDFYTAGKYREKGLQPFDMEKAIDERPSYVLFNGAEGALTGDKALHAKVGETVRIFVGNGGPNLVSSFHVIGAIFDQVRYEGGTNVQKNVQTTLIPAGGAAVVKFTARVPGSYVLVDHSIFRAFNKGAMAILKIDGAENKLVYSGKELDSVYLGDRAAPNMSAVTKATQASVSGTLTVQDQVQAGRALFAGTCSVCHQGNGAGLPGVFPPLAKSDFLAADPKRAMNIVLHGLNGKIKVNGQEYDSVMPPMTQLNDDEVANILTYVLNSWDNPGGRVSAEDVKKVRAQPAPAKAVAEH

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	2

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	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	809

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6. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

Domain ID domain_id	2yqbA01
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	2yqbA02
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	2yqbA03
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	127.849 Å
Unit-cell length b length_b	127.849 Å
Unit-cell length c length_c	86.628 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	9

Space group space_group	H 3
Space-group number int_tables_number	146
Crystal system crystal_system	—

Resolution resolution	1.410 Å
Low-resolution limit resolution_low	18.070 Å
R factor r_factor	0.1134
R_work r_work	0.1116
R_free r_free	0.1469

Structure of P93A variant of three-domain heme-Cu nitrite reductase from Ralstonia pickettii at 1.4 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

2yqb__assembly_1__model_1

2yqb__assembly_1__model_1 | I(q)

2yqb__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) 3 domains

CATH v4.4 (3 domains)

7. Citations (1)

Structure of P93A variant of three-domain heme-Cu nitrite reductase from Ralstonia pickettii at 1.4 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

2yqb__assembly_1__model_1

2yqb__assembly_1__model_1 | I(q)

2yqb__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) 3 domains

CATH v4.4 (3 domains)

7. Citations (1)