2iwk

Inhibitor-bound form of nitrous oxide reductase from Achromobacter Cycloclastes at 1.7 Angstrom resolution

Method: X-RAY DIFFRACTION

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

NITROUS OXIDE 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	COPPER (II) ION × 4 (MU-4-SULFIDO)-TETRA-NUCLEAR COPPER ION × 2 IODIDE ION × 15 CALCIUM ION × 28 CHLORIDE ION × 8 SODIUM ION × 30 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	NOSZ_ACHCY
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–642； UniProt 1–642 Author chain B； PDBConstruct 1–642； UniProt 1–642

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	2iwk
Deposition date deposition_date	2006-06-30
Structure title title	Inhibitor-bound form of nitrous oxide reductase from Achromobacter Cycloclastes at 1.7 Angstrom resolution
Keywords keywords	;METAL-BINDING, OXIDOREDUCTASE, DENITRIFICATION, NITROUS OXIDE BINDING, CATALYSIS, PERIPLASMIC ELECTRON GATING, COPPER CHEMISTRY, CALCIUM, COPPER ;; 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.

2iwk__assembly_1__model_1

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

Download this curve (.dat)

2iwk__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2iwk__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	30.92 Å
Rg (electron density)	30.46 Å
Total Rg	31.01 Å
Atom count	9355
Residues	1180
Excluded volume	167440 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2iwk__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 (8)

Entity 1 Entity 1 polymer

Description description	NITROUS OXIDE REDUCTASE
Molecular weight formula_weight	70993.1 kDa
EC 编号 ec_number	1.7.99.6
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	10214

MESKEHKGLSRRALFSATAGSAILAGTVGPAALSLGAAGLATPARAATGADGSVAPGKLDDYYGFWSSGQTGEMRILGIPSMRELMRVPVFNRCSATGWGQTNESIRIHQRTMTEKTKKQLAANGKKIHDNGDLHHVHMSFTDGKYDGRYLFMNDKANTRVARVRCDVMKTDAILEIPNAKGIHGMRPQKWPRSNYVFCNGEDEAPLVNDGSTMTDVATYVNIFTAVDADKWEVAWQVKVSGNLDNCDADYEGKWAFSTSYNSEMGMTLEEMTKSEMDHVVVFNIAEIEKAIKAGQYEEINGVKVVDGRKEAKSLFTRYIPIANNPHGCNMAPDRKHLCVAGKLSPTVTVLDVTKFDALFYDNAEPRSAVVAEPELGLGPLHTAFDGRGNAYTSLFLDSQVVKWNIDEAIRAYAGEKINPIKDKLDVQYQPGHLKTVMGETLDAANDWLVCLCKFSKDRFLNVGPLKPENDQLIDISGDKMVLVHDGPTFAEPHDAIAVSPSILPNIRSVWDRNDPLWAETRKQAEADEVDIDEWTEAVIRDGNKVRVYMTSVAPSFSQPSFTVKEGDEVTVIVTNLDEIDDLTHGFTMGNHGVAMEVGPQQTSSVTFVAANPGVYWYYCQWFCHALHMEMRGRMFVEPKGA

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	4

Entity 3 Entity 3 non-polymer

Description description	(MU-4-SULFIDO)-TETRA-NUCLEAR COPPER ION
Molecular weight formula_weight	286.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	IODIDE ION
Molecular weight formula_weight	126.9 kDa
Source method src_method	syn
Copy count entity_count	15

Entity 5 Entity 5 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	28

Entity 6 Entity 6 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 7 Entity 7 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	30

Entity 8 Entity 8 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	853

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6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d2iwka1
Class class	b — All beta proteins
Fold Fold fold	b.69 — 7-bladed beta-propeller
Superfamily Superfamily superfamily	b.69.3 — Nitrous oxide reductase, N-terminal domain
Family Family family	b.69.3.1 — Nitrous oxide reductase, N-terminal domain

Domain ID domain_id	d2iwka2
Class class	b — All beta proteins
Fold Fold fold	b.6 — Cupredoxin-like
Superfamily Superfamily superfamily	b.6.1 — Cupredoxins
Family Family family	b.6.1.0 — automated matches

Domain ID domain_id	d2iwkb1
Class class	b — All beta proteins
Fold Fold fold	b.69 — 7-bladed beta-propeller
Superfamily Superfamily superfamily	b.69.3 — Nitrous oxide reductase, N-terminal domain
Family Family family	b.69.3.1 — Nitrous oxide reductase, N-terminal domain

Domain ID domain_id	d2iwkb2
Class class	b — All beta proteins
Fold Fold fold	b.6 — Cupredoxin-like
Superfamily Superfamily superfamily	b.6.1 — Cupredoxins
Family Family family	b.6.1.0 — automated matches

CATH v4.4 (4 domains)

Domain ID domain_id	2iwkA01
Class class	2 — Mainly Beta
Architecture architecture	130 — 7 Propeller
Topology topology	10 — Methylamine Dehydrogenase; Chain H
Homologous superfamily homologous superfamily	10 — YVTN repeat-like/Quinoprotein amine dehydrogenase

Domain ID domain_id	2iwkA02
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	2iwkB01
Class class	2 — Mainly Beta
Architecture architecture	130 — 7 Propeller
Topology topology	10 — Methylamine Dehydrogenase; Chain H
Homologous superfamily homologous superfamily	10 — YVTN repeat-like/Quinoprotein amine dehydrogenase

Domain ID domain_id	2iwkB02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	420 — Cupredoxins - blue copper proteins

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Unit-cell length a length_a	71.114 Å
Unit-cell length b length_b	120.913 Å
Unit-cell length c length_c	137.343 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	8

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	50.000 Å
R factor r_factor	0.1700
R_work r_work	0.1680
R_free r_free	0.2070

Inhibitor-bound form of nitrous oxide reductase from Achromobacter Cycloclastes at 1.7 Angstrom resolution

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

NITROUS OXIDE 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

2iwk__assembly_1__model_1

2iwk__assembly_1__model_1 | I(q)

2iwk__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 (8)

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 non-polymer

Entity 8 Entity 8 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)

Inhibitor-bound form of nitrous oxide reductase from Achromobacter Cycloclastes at 1.7 Angstrom resolution

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

NITROUS OXIDE 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

2iwk__assembly_1__model_1

2iwk__assembly_1__model_1 | I(q)

2iwk__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 (8)

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 non-polymer

Entity 8 Entity 8 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)