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2ot4

Structure of a hexameric multiheme c nitrite reductase from the extremophile bacterium Thiolkalivibrio nitratireducens

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

Eight-heme nitrite reductase

OrganismNot specified

UniProt Q5F2I3

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein homooligomer Homooligomer Protein 6 CALCIUM ION × 6 HEME C × 48 (4R)-2-METHYLPENTANE-2,4-DIOL × 12 (4S)-2-METHYL-2,4-PENTANEDIOL × 9 CITRIC ACID × 3 water × 6 Consistent with protein count

Other States of the Same Protein in the Database

Monomer

None

Homodimer

None

Homotetramer

None

Other homooligomers
2ot4 2zo5 3d1i 3f29 3fo3 3gm6 3lg1 3lgq 3mmo 3owm 3rkh 3s7w

20 assemblies; showing the first 12

Heteromeric or nucleic-acid complex

None

View Construct and Data Evidence
UniProt name Q5F2I3_9GAMM
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–525； UniProt 29–553 Author chain B； PDBConstruct 1–525； UniProt 29–553

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_id2ot4
Deposition date deposition_date2007-02-07
Structure title titleStructure of a hexameric multiheme c nitrite reductase from the extremophile bacterium Thiolkalivibrio nitratireducens
Keywords keywordscytochrome c nitrite reductase, NrfA, sulfite reductase, OXIDOREDUCTASE; 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.

2ot4__assembly_1__model_1

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

Download this curve (.dat)

2ot4__assembly_1__model_1 | I(q)

10-2 10-1 106 107 108 109 q (1/Angstrom) I(q)
100 plotted points; both axes use logarithmic scales.

2ot4__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）46.77 Å
Rg (electron density)45.82 Å
Total Rg46.10 Å
Atom count51873
Residues3120
Excluded volume473570 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 2ot4__assembly_1__model_1 hexameric （6） 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)

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6. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

Domain ID domain_id2ot4A01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology287 — Helix Hairpins
Homologous superfamily homologous superfamily3080 —
Domain ID domain_id2ot4A02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology1130 — Flavocytochrome C3; Chain A, domain 2
Homologous superfamily homologous superfamily10 — Flavocytochrome C3; Chain A
Domain ID domain_id2ot4A03
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_id2ot4B01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology287 — Helix Hairpins
Homologous superfamily homologous superfamily3080 —
Domain ID domain_id2ot4B02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology1130 — Flavocytochrome C3; Chain A, domain 2
Homologous superfamily homologous superfamily10 — Flavocytochrome C3; Chain A
Domain ID domain_id2ot4B03
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 (5)