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3d9e

Nitroalkane oxidase: active site mutant D402N crystallized with 1-nitrooctane

Method: X-RAY DIFFRACTION
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Nitroalkane oxidase

Fusarium oxysporum

UniProt Q8X1D8

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein homooligomer Homooligomer Protein 4 FLAVIN-ADENINE DINUCLEOTIDE × 4 1-nitrooctane × 4 GLYCEROL × 4 water × 4 Consistent with protein count

Other States of the Same Protein in the Database

Monomer

None

Homodimer

None

Homotetramer
2c0u 2c12 2c12 2reh 2zaf 3d9d 3d9e 3d9f 3d9g 3fcj

10 assemblies

Other homooligomers

None

Heteromeric or nucleic-acid complex

None

View Construct and Data Evidence
UniProt name Q8X1D8_FUSOX
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–438； UniProt 2–439 Author chain B； PDBConstruct 1–438； UniProt 2–439 Author chain C； PDBConstruct 1–438； UniProt 2–439 Author chain D； PDBConstruct 1–438； UniProt 2–439

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_id3d9e
Deposition date deposition_date2008-05-27
Structure title titleNitroalkane oxidase: active site mutant D402N crystallized with 1-nitrooctane
Keywords keywordsOXIDOREDUCTASE, FLAVOENZYME, NITROALKANE, ACYL-COA DEHYDROGENASE, LONG CELL EDGE, FAD, INHIBITOR, FLAVOPROTEIN; OXIDOREDUCTASE
Experimental Method methodX-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.

3d9e__assembly_1__model_1

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

Download this curve (.dat)

3d9e__assembly_1__model_1 | I(q)

10-2 10-1 106 107 108 q (1/Angstrom) I(q)
100 plotted points; both axes use logarithmic scales.

3d9e__assembly_1__model_1 | P(r) · Pending

The new assembly/model P(r) has not been calculated yet This placeholder does not display legacy data r (Angstrom) P(r)
P(r) will be calculated and displayed separately for the same assembly/model.
Rg（Guinier）35.64 Å
Rg (electron density)34.82 Å
Total Rg35.23 Å
Atom count13499
Residues1723
Excluded volume240830 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 3d9e__assembly_1__model_1 tetrameric （4） 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)

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6. Fold Classification (SCOP + CATH) 20 domains

SCOP 2.08 (8 domains)

Domain ID domain_idd3d9ea1
Class classe — Multi-domain proteins (alpha and beta)
Fold Fold folde.6 — Acyl-CoA dehydrogenase NM domain-like
Superfamily Superfamily superfamilye.6.1 — Acyl-CoA dehydrogenase NM domain-like
Family Family familye.6.1.1 — Medium chain acyl-CoA dehydrogenase, NM (N-terminal and middle) domains
Domain ID domain_idd3d9ea2
Class classa — All alpha proteins
Fold Fold folda.29 — Bromodomain-like
Superfamily Superfamily superfamilya.29.3 — Acyl-CoA dehydrogenase C-terminal domain-like
Family Family familya.29.3.1 — Medium chain acyl-CoA dehydrogenase-like, C-terminal domain
Domain ID domain_idd3d9eb1
Class classe — Multi-domain proteins (alpha and beta)
Fold Fold folde.6 — Acyl-CoA dehydrogenase NM domain-like
Superfamily Superfamily superfamilye.6.1 — Acyl-CoA dehydrogenase NM domain-like
Family Family familye.6.1.1 — Medium chain acyl-CoA dehydrogenase, NM (N-terminal and middle) domains
Domain ID domain_idd3d9eb2
Class classa — All alpha proteins
Fold Fold folda.29 — Bromodomain-like
Superfamily Superfamily superfamilya.29.3 — Acyl-CoA dehydrogenase C-terminal domain-like
Family Family familya.29.3.1 — Medium chain acyl-CoA dehydrogenase-like, C-terminal domain
Domain ID domain_idd3d9ec1
Class classe — Multi-domain proteins (alpha and beta)
Fold Fold folde.6 — Acyl-CoA dehydrogenase NM domain-like
Superfamily Superfamily superfamilye.6.1 — Acyl-CoA dehydrogenase NM domain-like
Family Family familye.6.1.1 — Medium chain acyl-CoA dehydrogenase, NM (N-terminal and middle) domains
Domain ID domain_idd3d9ec2
Class classa — All alpha proteins
Fold Fold folda.29 — Bromodomain-like
Superfamily Superfamily superfamilya.29.3 — Acyl-CoA dehydrogenase C-terminal domain-like
Family Family familya.29.3.1 — Medium chain acyl-CoA dehydrogenase-like, C-terminal domain
Domain ID domain_idd3d9ed1
Class classe — Multi-domain proteins (alpha and beta)
Fold Fold folde.6 — Acyl-CoA dehydrogenase NM domain-like
Superfamily Superfamily superfamilye.6.1 — Acyl-CoA dehydrogenase NM domain-like
Family Family familye.6.1.1 — Medium chain acyl-CoA dehydrogenase, NM (N-terminal and middle) domains
Domain ID domain_idd3d9ed2
Class classa — All alpha proteins
Fold Fold folda.29 — Bromodomain-like
Superfamily Superfamily superfamilya.29.3 — Acyl-CoA dehydrogenase C-terminal domain-like
Family Family familya.29.3.1 — Medium chain acyl-CoA dehydrogenase-like, C-terminal domain

CATH v4.4 (12 domains)

Domain ID domain_id3d9eA01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology540 — Butyryl-Coa Dehydrogenase, subunit A; domain 1
Homologous superfamily homologous superfamily10 — Acyl-CoA dehydrogenase/oxidase, N-terminal domain
Domain ID domain_id3d9eA02
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology110 — Butyryl-CoA Dehydrogenase, subunit A; domain 2
Homologous superfamily homologous superfamily10 — Butyryl-CoA Dehydrogenase, subunit A, domain 2
Domain ID domain_id3d9eA03
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology140 — Butyryl-CoA Dehydrogenase, subunit A; domain 3
Homologous superfamily homologous superfamily10 — Butyryl-CoA Dehydrogenase, subunit A, domain 3
Domain ID domain_id3d9eB01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology540 — Butyryl-Coa Dehydrogenase, subunit A; domain 1
Homologous superfamily homologous superfamily10 — Acyl-CoA dehydrogenase/oxidase, N-terminal domain
Domain ID domain_id3d9eB02
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology110 — Butyryl-CoA Dehydrogenase, subunit A; domain 2
Homologous superfamily homologous superfamily10 — Butyryl-CoA Dehydrogenase, subunit A, domain 2
Domain ID domain_id3d9eB03
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology140 — Butyryl-CoA Dehydrogenase, subunit A; domain 3
Homologous superfamily homologous superfamily10 — Butyryl-CoA Dehydrogenase, subunit A, domain 3
Domain ID domain_id3d9eC01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology540 — Butyryl-Coa Dehydrogenase, subunit A; domain 1
Homologous superfamily homologous superfamily10 — Acyl-CoA dehydrogenase/oxidase, N-terminal domain
Domain ID domain_id3d9eC02
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology110 — Butyryl-CoA Dehydrogenase, subunit A; domain 2
Homologous superfamily homologous superfamily10 — Butyryl-CoA Dehydrogenase, subunit A, domain 2
Domain ID domain_id3d9eC03
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology140 — Butyryl-CoA Dehydrogenase, subunit A; domain 3
Homologous superfamily homologous superfamily10 — Butyryl-CoA Dehydrogenase, subunit A, domain 3
Domain ID domain_id3d9eD01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology540 — Butyryl-Coa Dehydrogenase, subunit A; domain 1
Homologous superfamily homologous superfamily10 — Acyl-CoA dehydrogenase/oxidase, N-terminal domain
Domain ID domain_id3d9eD02
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology110 — Butyryl-CoA Dehydrogenase, subunit A; domain 2
Homologous superfamily homologous superfamily10 — Butyryl-CoA Dehydrogenase, subunit A, domain 2
Domain ID domain_id3d9eD03
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology140 — Butyryl-CoA Dehydrogenase, subunit A; domain 3
Homologous superfamily homologous superfamily10 — Butyryl-CoA Dehydrogenase, subunit A, domain 3
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7. Citations (3)