SAXSdb — 2zoo

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

Probable nitrite reductase

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Homooligomer	Protein 3 其他Polymer 3	beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose × 3 COPPER (II) ION × 6 PROTOPORPHYRIN IX CONTAINING FE × 3 SULFATE ION × 9 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q3IGF7_PSEHT
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–442； UniProt 26–467

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	2zoo
Deposition date deposition_date	2008-05-27
Structure title title	Crystal structure of nitrite reductase from Pseudoalteromonas haloplanktis TAC125
Keywords keywords	nitrite, electron transfer, Electron transport, Heme, Iron, Metal-binding, Oxidoreductase, Transport; 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.

2zoo__assembly_1__model_1

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

Download this curve (.dat)

2zoo__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2zoo__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	32.53 Å
Rg (electron density)	31.25 Å
Total Rg	32.04 Å
Atom count	10227
Residues	1314
Excluded volume	180960 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2zoo__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 (6)

Entity 1 Entity 1 polymer

Description description	Probable nitrite reductase
Molecular weight formula_weight	47620.3 kDa
EC 编号 ec_number	1.7.99.3, 1.7.2.1
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	3811

ASNLKTEQAILTPPPMVPPAINRDHSAKVVINLETREQVGRIADGVEYVFWSFGETVPGSFIRVREGDEIEFNLSNHPSSKMPHNIDLHAVTGPGGGAESSFTAPGHTSTFNFKALNPGLYIYHCATAPVGMHIANGMYGLILVEPKEGLAPVDREYYLVQGDFYTKGEFGEAGLQPFDMAKAIDEDADYVVFNGSVGSTTDENSLTAKVGETVRLYIGNGGPNLVSSFHVIGEIFDTVYVEGGSLKNHNVQTTLIPAGGAAIVEFKVEVPGTFILVDHSIFRAFNKGALAMLKVEGPDDHSIFTGKTAENVYLPEGSAIQSLDNTFTKITANNKDEQIRFGQRVYEANCMACHQANGEGIPGAFPPLAKSDYLNNNPLLGVNAIIKGLSGPIKVNNVNYNGVMPAMNLNDEDIANVITFVLNNWDNAGGKVSAEQVAKQRK

Entity 2 Entity 2 branched

Description description	beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose
Molecular weight formula_weight	342.3 kDa
Source method src_method	man
Copy count entity_count	1

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	2

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 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	402

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6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	2zooA01
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	2zooA02
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	180.338 Å
Unit-cell length b length_b	180.338 Å
Unit-cell length c length_c	180.338 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	24

Space group space_group	P 41 3 2
Space-group number int_tables_number	213
Crystal system crystal_system	—

Resolution resolution	1.950 Å
Low-resolution limit resolution_low	8.000 Å
R factor r_factor	0.1677
R_work r_work	0.1656
R_free r_free	0.1860

Crystal structure of nitrite reductase from Pseudoalteromonas haloplanktis TAC125

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

Probable 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

2zoo__assembly_1__model_1

2zoo__assembly_1__model_1 | I(q)

2zoo__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 (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 branched

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)

Crystal structure of nitrite reductase from Pseudoalteromonas haloplanktis TAC125

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

Probable 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

2zoo__assembly_1__model_1

2zoo__assembly_1__model_1 | I(q)

2zoo__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 (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 branched

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)