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3bkf

Zinc-bound C-terminal Domain of NikR

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

Nickel-responsive regulator

Escherichia coli

UniProt P0A6Z6

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein homooligomer Homooligomer Protein 4 ZINC ION × 8 water × 4 Consistent with protein count
2 Protein homooligomer Homooligomer Protein 2 ZINC ION × 4 water × 2 Consistent with protein count

Other States of the Same Protein in the Database

Monomer

None

Homodimer
3bkf 3bkt 3bkt 3bku 3bku

5 assemblies

Homotetramer
1q5v 1q5y 2hza 3bkf 3bkt 3bku

6 assemblies

Other homooligomers

None

Heteromeric or nucleic-acid complex
2hzv 2hzv

2 assemblies

View Construct and Data Evidence
UniProt name NIKR_ECOLI
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–86； UniProt 48–133

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_id3bkf
Deposition date deposition_date2007-12-06
Structure title titleZinc-bound C-terminal Domain of NikR
Keywords keywords;NikR, nickel regulatory protein, transcription factor, beta sandwich, DNA-binding, Metal-binding, Repressor, Transcription regulation, METAL BINDING PROTEIN ;; METAL BINDING PROTEIN
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.

3bkf__assembly_1__model_1

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

Download this curve (.dat)

3bkf__assembly_1__model_1 | I(q)

10-2 10-1 105 106 107 q (1/Angstrom) I(q)
100 plotted points; both axes use logarithmic scales.

3bkf__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）19.61 Å
Rg (electron density)18.09 Å
Total Rg18.85 Å
Atom count2040
Residues264
Excluded volume35787 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 3bkf__assembly_1__model_1 tetrameric （4） Success 4.1.3-1-20251215 (887e7ef) View Download
2 1 3bkf__assembly_2__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 (3)

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6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd3bkfa1
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.58 — Ferredoxin-like
Superfamily Superfamily superfamilyd.58.18 — ACT-like
Family Family familyd.58.18.4 — Nickel responsive regulator NikR, C-terminal domain

CATH v4.4 (1 domains)

Domain ID domain_id3bkfA00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily1150 — ACT-like. Chain A, domain 2
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7. Citations (1)