SAXSdb — 1dy7

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

NITRITE REDUCTASE

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	HEME D × 2 CARBON MONOXIDE × 2 GLYCEROL × 3 SULFATE ION × 3 HEME C × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	NIRS_PARDT
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–567； UniProt 30–596 Author chain B； PDBConstruct 1–567； UniProt 30–596

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	1dy7
Deposition date deposition_date	2000-01-28
Structure title title	Cytochrome cd1 Nitrite Reductase, CO complex
Keywords keywords	ENZYME, NITRITE REDUCTASE, 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.

1dy7__assembly_1__model_1

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

Download this curve (.dat)

1dy7__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1dy7__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	33.17 Å
Rg (electron density)	32.68 Å
Total Rg	33.09 Å
Atom count	7745
Residues	970
Excluded volume	136900 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1dy7__assembly_1__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 (7)

Entity 1 Entity 1 polymer

Description description	NITRITE REDUCTASE
Molecular weight formula_weight	62546.5 kDa
EC 编号 ec_number	1.7.2.1, 1.7.99.1
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	8592

QEQVAPPKDPAAALEDHKTRTDNRYEPSLDNLAQQDVAAPGAPEGVSALSDAQYNEANKIYFERCAGCHGVLRKGATGKALTPDLTRDLGFDYLQSFITYGSPAGMPNWGTSGELSAEQVDLMANYLLLDPAAPPEFGMKEMRESWKVHVAPEDRPTQQENDWDLENLFSVTLRDAGQIALIDGATYEIKSVLDTGYAVHISRLSASGRYLFVIGRDGKVNMIDLWMKEPTTVAEIKIGSEARSIETSKMEGWEDKYAIAGAYWPPQYVIMDGETLEPKKIQSTRGMTYDEQEYHPEPRVAAILASHYRPEFIVNVKETGKILLVDYTDLDNLKTTEISAERFLHDGGLDGSHRYFITAANARNKLVVIDTKEGKLVAIEDTGGQTPHPGRGANFVHPTFGPVWATSHMGDDSVALIGTDPEGHPDNAWKILDSFPALGGGSLFIKTHPNSQYLYVDATLNPEAEISGSVAVFDIKAMTGDGSDPEFKTLPIAEWAGITEGQPRVVQGEFNKDGTEVWFSVWNGKDQESALVVVDDKTLELKHVIKDERLVTPTGKFNVYNTMTDTY

Entity 2 Entity 2 non-polymer

Description description	HEME D
Molecular weight formula_weight	712.5 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	CARBON MONOXIDE
Molecular weight formula_weight	28.0 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	3

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 non-polymer

Description description	HEME C
Molecular weight formula_weight	618.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 7 Entity 7 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	847

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6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d1dy7a_
Class class	b — All beta proteins
Fold Fold fold	b.70 — 8-bladed beta-propeller
Superfamily Superfamily superfamily	b.70.2 — C-terminal (heme d1) domain of cytochrome cd1-nitrite reductase
Family Family family	b.70.2.1 — C-terminal (heme d1) domain of cytochrome cd1-nitrite reductase

Domain ID domain_id	d1dy7b1
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.3.1.2 — N-terminal (heme c) domain of cytochrome cd1-nitrite reductase

Domain ID domain_id	d1dy7b2
Class class	b — All beta proteins
Fold Fold fold	b.70 — 8-bladed beta-propeller
Superfamily Superfamily superfamily	b.70.2 — C-terminal (heme d1) domain of cytochrome cd1-nitrite reductase
Family Family family	b.70.2.1 — C-terminal (heme d1) domain of cytochrome cd1-nitrite reductase

CATH v4.4 (3 domains)

Domain ID domain_id	1dy7A00
Class class	2 — Mainly Beta
Architecture architecture	140 — 8 Propeller
Topology topology	10 — Methanol Dehydrogenase; Chain A
Homologous superfamily homologous superfamily	20 — C-terminal (heme d1) domain of cytochrome cd1-nitrite reductase

Domain ID domain_id	1dy7B01
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	1dy7B02
Class class	2 — Mainly Beta
Architecture architecture	140 — 8 Propeller
Topology topology	10 — Methanol Dehydrogenase; Chain A
Homologous superfamily homologous superfamily	20 — C-terminal (heme d1) domain of cytochrome cd1-nitrite reductase

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Unit-cell length a length_a	106.940 Å
Unit-cell length b length_b	61.040 Å
Unit-cell length c length_c	100.390 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	111.77 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	1.600 Å
Low-resolution limit resolution_low	30.000 Å
R factor r_factor	—
R_work r_work	0.1780
R_free r_free	0.1990

Cytochrome cd1 Nitrite Reductase, CO complex

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

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

1dy7__assembly_1__model_1

1dy7__assembly_1__model_1 | I(q)

1dy7__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 (7)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

CATH v4.4 (3 domains)

7. Citations (2)

Cytochrome cd1 Nitrite Reductase, CO complex

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

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

1dy7__assembly_1__model_1

1dy7__assembly_1__model_1 | I(q)

1dy7__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 (7)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

CATH v4.4 (3 domains)

7. Citations (2)