1ych

X-ray Crystal Structures of Moorella thermoacetica FprA. Novel Diiron Site Structure and Mechanistic Insights into a Scavenging Nitric Oxide Reductase

Method: X-RAY DIFFRACTION

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

Nitric oxide reductase

Moorella thermoacetica

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	ZINC ION × 4 MU-OXO-DIIRON × 2 FLAVIN MONONUCLEOTIDE × 2 water × 2	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	ZINC ION × 4 MU-OXO-DIIRON × 2 FLAVIN MONONUCLEOTIDE × 2 water × 2	Consistent with protein count
3	Protein homooligomer	Homooligomer	Protein 4	ZINC ION × 8 MU-OXO-DIIRON × 4 FLAVIN MONONUCLEOTIDE × 4 water × 4	Consistent with protein count
4	Protein homooligomer	Homooligomer	Protein 2	ZINC ION × 4 MU-OXO-DIIRON × 2 FLAVIN MONONUCLEOTIDE × 2 water × 2	Consistent with protein count
5	Protein homooligomer	Homooligomer	Protein 2	ZINC ION × 4 MU-OXO-DIIRON × 2 FLAVIN MONONUCLEOTIDE × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	FPRA_MOOTH
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–398； UniProt 2–399 Author chain B； PDBConstruct 1–398； UniProt 2–399 Author chain C； PDBConstruct 1–398； UniProt 2–399 Author chain D； PDBConstruct 1–398； UniProt 2–399

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	1ych
Deposition date deposition_date	2004-12-22
Structure title title	X-ray Crystal Structures of Moorella thermoacetica FprA. Novel Diiron Site Structure and Mechanistic Insights into a Scavenging Nitric Oxide Reductase
Keywords keywords	Nitric Oxide, reductase, diiron site, 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.

1ych__assembly_1__model_1

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

Download this curve (.dat)

1ych__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1ych__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	31.47 Å
Rg (electron density)	31.21 Å
Total Rg	31.78 Å
Atom count	6302
Residues	796
Excluded volume	113130 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1ych__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1ych__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`1ych__assembly_3__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`1ych__assembly_4__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
5	1	`1ych__assembly_5__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 (5)

Entity 1 Entity 1 polymer

Description description	Nitric oxide reductase
Molecular weight formula_weight	44219.8 kDa
EC 编号 ec_number	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	12886

SQPVAITDGIYWVGAVDWNIRYFHGPAFSTHRGTTYNAYLIVDDKTALVDTVYEPFKEELIAKLKQIKDPVKLDYLVVNHTESDHAGAFPAIMELCPDAHVLCTQRAFDSLKAHYSHIDFNYTIVKTGTSVSLGKRSLTFIEAPMLHWPDSMFTYVPEEALLLPNDAFGQHIATSVRFDDQVDAGLIMDEAAKYYANILMPFSNLITKKLDEIQKINLAIKTIAPSHGIIWRKDPGRIIEAYARWAEGQGKAKAVIAYDTMWLSTEKMAHALMDGLVAGGCEVKLFKLSVSDRNDVIKEILDARAVLVGSPTINNDILPVVSPLLDDLVGLRPKNKVGLAFGAYGWGGGAQKILEERLKAAKIELIAEPGPTVQWVPRGEDLQRCYELGRKIAARIAD

Source Source

Source organism organism	Moorella thermoacetica
NCBI taxonomy ID ncbi_taxonomy_id	1525
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 3 Entity 3 non-polymer

Description description	MU-OXO-DIIRON
Molecular weight formula_weight	127.7 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 non-polymer

Description description	FLAVIN MONONUCLEOTIDE
Molecular weight formula_weight	456.3 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	282

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6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d1ycha1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.23 — Flavodoxin-like
Superfamily Superfamily superfamily	c.23.5 — Flavoproteins
Family Family family	c.23.5.1 — Flavodoxin-related

Domain ID domain_id	d1ycha2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.157 — Metallo-hydrolase/oxidoreductase
Superfamily Superfamily superfamily	d.157.1 — Metallo-hydrolase/oxidoreductase
Family Family family	d.157.1.3 — ROO N-terminal domain-like

Domain ID domain_id	d1ychb1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.23 — Flavodoxin-like
Superfamily Superfamily superfamily	c.23.5 — Flavoproteins
Family Family family	c.23.5.1 — Flavodoxin-related

Domain ID domain_id	d1ychb2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.157 — Metallo-hydrolase/oxidoreductase
Superfamily Superfamily superfamily	d.157.1 — Metallo-hydrolase/oxidoreductase
Family Family family	d.157.1.3 — ROO N-terminal domain-like

Domain ID domain_id	d1ychc1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.23 — Flavodoxin-like
Superfamily Superfamily superfamily	c.23.5 — Flavoproteins
Family Family family	c.23.5.1 — Flavodoxin-related

Domain ID domain_id	d1ychc2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.157 — Metallo-hydrolase/oxidoreductase
Superfamily Superfamily superfamily	d.157.1 — Metallo-hydrolase/oxidoreductase
Family Family family	d.157.1.3 — ROO N-terminal domain-like

Domain ID domain_id	d1ychd1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.23 — Flavodoxin-like
Superfamily Superfamily superfamily	c.23.5 — Flavoproteins
Family Family family	c.23.5.1 — Flavodoxin-related

Domain ID domain_id	d1ychd2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.157 — Metallo-hydrolase/oxidoreductase
Superfamily Superfamily superfamily	d.157.1 — Metallo-hydrolase/oxidoreductase
Family Family family	d.157.1.3 — ROO N-terminal domain-like

CATH v4.4 (8 domains)

Domain ID domain_id	1ychA01
Class class	3 — Alpha Beta
Architecture architecture	60 — 4-Layer Sandwich
Topology topology	15 — Metallo-beta-lactamase; Chain A
Homologous superfamily homologous superfamily	10 — Ribonuclease Z/Hydroxyacylglutathione hydrolase-like

Domain ID domain_id	1ychA02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	360 — Flavodoxin domain

Domain ID domain_id	1ychB01
Class class	3 — Alpha Beta
Architecture architecture	60 — 4-Layer Sandwich
Topology topology	15 — Metallo-beta-lactamase; Chain A
Homologous superfamily homologous superfamily	10 — Ribonuclease Z/Hydroxyacylglutathione hydrolase-like

Domain ID domain_id	1ychB02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	360 — Flavodoxin domain

Domain ID domain_id	1ychC01
Class class	3 — Alpha Beta
Architecture architecture	60 — 4-Layer Sandwich
Topology topology	15 — Metallo-beta-lactamase; Chain A
Homologous superfamily homologous superfamily	10 — Ribonuclease Z/Hydroxyacylglutathione hydrolase-like

Domain ID domain_id	1ychC02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	360 — Flavodoxin domain

Domain ID domain_id	1ychD01
Class class	3 — Alpha Beta
Architecture architecture	60 — 4-Layer Sandwich
Topology topology	15 — Metallo-beta-lactamase; Chain A
Homologous superfamily homologous superfamily	10 — Ribonuclease Z/Hydroxyacylglutathione hydrolase-like

Domain ID domain_id	1ychD02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	360 — Flavodoxin domain

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Unit-cell length a length_a	160.327 Å
Unit-cell length b length_b	160.327 Å
Unit-cell length c length_c	279.144 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	32

Space group space_group	P 43 21 2
Space-group number int_tables_number	96
Crystal system crystal_system	—

Resolution resolution	2.800 Å
Low-resolution limit resolution_low	43.910 Å
R factor r_factor	0.2240
R_work r_work	0.2240
R_free r_free	0.2450

X-ray Crystal Structures of Moorella thermoacetica FprA. Novel Diiron Site Structure and Mechanistic Insights into a Scavenging Nitric Oxide Reductase

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

Nitric 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

1ych__assembly_1__model_1

1ych__assembly_1__model_1 | I(q)

1ych__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 (5)

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 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

CATH v4.4 (8 domains)

7. Citations (1)

X-ray Crystal Structures of Moorella thermoacetica FprA. Novel Diiron Site Structure and Mechanistic Insights into a Scavenging Nitric Oxide Reductase

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

Nitric 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

1ych__assembly_1__model_1

1ych__assembly_1__model_1 | I(q)

1ych__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 (5)

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 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

CATH v4.4 (8 domains)

7. Citations (1)