SAXSdb — 3h8i

▼

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

NADH oxidase

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	FLAVIN-ADENINE DINUCLEOTIDE × 2 trisulfane × 2 PHOSPHATE ION × 9 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q7ZAG8_ACIAM
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–409； UniProt 1–409 Author chain B； PDBConstruct 1–409； UniProt 1–409

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	3h8i
Deposition date deposition_date	2009-04-29
Structure title title	The first X-ray structure of a sulfide:quinone oxidoreductase: Insights into sulfide oxidation mechanism
Keywords keywords	Membrane protein, rossman-like fold, Oxidoreductase; OXIDOREDUCTASE
Experimental Method method	X-RAY DIFFRACTION

▼

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.

3h8i__assembly_1__model_1

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

Download this curve (.dat)

3h8i__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3h8i__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	29.79 Å
Rg (electron density)	28.80 Å
Total Rg	29.52 Å
Atom count	5667
Residues	712
Excluded volume	101020 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3h8i__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	NADH oxidase
Molecular weight formula_weight	45174.6 kDa
EC 编号 ec_number	1.6.99.3
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	5916

MTKVLVLGGRFGALTAAYTLKRLVGSKADVKVINKSRFSYFRPALPHVAIGVRDVDELKVDLSEALPEKGIQFQEGTVEKIDAKSSMVYYTKPDGSMAEEEYDYVIVGIGAHLATELVKGWDKYGYSVCEPEFATKLREKLESFQGGNIAIGSGPFYQGHNPKPKVPENFVPNADSACEGPVFEMSLMLHGYFKKKGMLDKVHVTVFSPGEYLSDLSPNSRKAVASIYNQLGIKLVHNFKIKEIREHEIVDEKGNTIPADITILLPPYTGNPALKNSTPDLVDDGGFIPTDLNMVSIKYDNVYAVGDANSMTVPKLGYLAVMTGRIAAQHLANRLGVPTKVDKYYPTIVCVADNPYEGYAVSVKDDTWYGGTVSIADPAAVNHLKKELFTKYYMWTKGDMALEKFLASW

Entity 2 Entity 2 non-polymer

Description description	FLAVIN-ADENINE DINUCLEOTIDE
Molecular weight formula_weight	785.5 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	trisulfane
Molecular weight formula_weight	98.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	PHOSPHATE ION
Molecular weight formula_weight	95.0 kDa
Source method src_method	syn
Copy count entity_count	9

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	171

▼

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	3h8iA01
Class class	3 — Alpha Beta
Architecture architecture	50 — 3-Layer(bba) Sandwich
Topology topology	50 — FAD/NAD(P)-binding domain
Homologous superfamily homologous superfamily	60 — FAD/NAD(P)-binding domain

Domain ID domain_id	3h8iA02
Class class	3 — Alpha Beta
Architecture architecture	50 — 3-Layer(bba) Sandwich
Topology topology	50 — FAD/NAD(P)-binding domain
Homologous superfamily homologous superfamily	60 — FAD/NAD(P)-binding domain

Domain ID domain_id	3h8iB01
Class class	3 — Alpha Beta
Architecture architecture	50 — 3-Layer(bba) Sandwich
Topology topology	50 — FAD/NAD(P)-binding domain
Homologous superfamily homologous superfamily	60 — FAD/NAD(P)-binding domain

Domain ID domain_id	3h8iB02
Class class	3 — Alpha Beta
Architecture architecture	50 — 3-Layer(bba) Sandwich
Topology topology	50 — FAD/NAD(P)-binding domain
Homologous superfamily homologous superfamily	60 — FAD/NAD(P)-binding domain

▶

Unit-cell length a length_a	178.550 Å
Unit-cell length b length_b	178.550 Å
Unit-cell length c length_c	162.310 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	24

Space group space_group	P 65 2 2
Space-group number int_tables_number	179
Crystal system crystal_system	—

Resolution resolution	2.650 Å
Low-resolution limit resolution_low	26.660 Å
R factor r_factor	0.1970
R_work r_work	0.1955
R_free r_free	0.2246

The first X-ray structure of a sulfide:quinone oxidoreductase: Insights into sulfide oxidation mechanism

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

NADH oxidase

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

3h8i__assembly_1__model_1

3h8i__assembly_1__model_1 | I(q)

3h8i__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

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) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)

The first X-ray structure of a sulfide:quinone oxidoreductase: Insights into sulfide oxidation mechanism

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

NADH oxidase

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

3h8i__assembly_1__model_1

3h8i__assembly_1__model_1 | I(q)

3h8i__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

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) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)