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2kmt

NMR solution structure of Vibrio fischeri CcdB

Method: SOLUTION NMR
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1. Protein Identity and Related Structures Protein Identity & Related Structures

CcdB

Vibrio fischeri

UniProt Q84B82

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein homooligomer Homooligomer Protein 2 No other associated polymer Consistent with protein count

Other States of the Same Protein in the Database

Monomer

None

Homodimer
2kmt 3jrz 3jsc

3 assemblies

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
3tcj 4ely

2 assemblies

View Construct and Data Evidence
UniProt name Q84B82_VIBFI
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–105； UniProt 1–105 Author chain B； PDBConstruct 1–105； UniProt 1–105

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_id2kmt
Deposition date deposition_date2009-08-04
Structure title titleNMR solution structure of Vibrio fischeri CcdB
Keywords keywordsToxin; TOXIN
Experimental Method methodSOLUTION NMR
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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.

2kmt__assembly_1__model_1

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

Download this curve (.dat)

2kmt__assembly_1__model_1 | I(q)

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

2kmt__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）18.25 Å
Rg (electron density)17.12 Å
Total Rg18.09 Å
Atom count3386
Residues210
Excluded volume30292 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 2kmt__assembly_1__model_1 dimeric （2） Success 4.1.3-1-20251215 (887e7ef) View Download
1 2 2kmt__assembly_1__model_2 dimeric （2） Success 4.1.3-1-20251215 (887e7ef) View Download
1 3 2kmt__assembly_1__model_3 dimeric （2） Success 4.1.3-1-20251215 (887e7ef) View Download
1 4 2kmt__assembly_1__model_4 dimeric （2） Success 4.1.3-1-20251215 (887e7ef) View Download
1 5 2kmt__assembly_1__model_5 dimeric （2） Success 4.1.3-1-20251215 (887e7ef) View Download
1 6 2kmt__assembly_1__model_6 dimeric （2） Success 4.1.3-1-20251215 (887e7ef) View Download
1 7 2kmt__assembly_1__model_7 dimeric （2） Success 4.1.3-1-20251215 (887e7ef) View Download
1 8 2kmt__assembly_1__model_8 dimeric （2） Success 4.1.3-1-20251215 (887e7ef) View Download
1 9 2kmt__assembly_1__model_9 dimeric （2） Success 4.1.3-1-20251215 (887e7ef) View Download
1 10 2kmt__assembly_1__model_10 dimeric （2） Success 4.1.3-1-20251215 (887e7ef) View Download
1 11 2kmt__assembly_1__model_11 dimeric （2） Success 4.1.3-1-20251215 (887e7ef) View Download
1 12 2kmt__assembly_1__model_12 dimeric （2） Success 4.1.3-1-20251215 (887e7ef) View Download
1 13 2kmt__assembly_1__model_13 dimeric （2） Success 4.1.3-1-20251215 (887e7ef) View Download
1 14 2kmt__assembly_1__model_14 dimeric （2） Success 4.1.3-1-20251215 (887e7ef) View Download
1 15 2kmt__assembly_1__model_15 dimeric （2） Success 4.1.3-1-20251215 (887e7ef) View Download
1 16 2kmt__assembly_1__model_16 dimeric （2） Success 4.1.3-1-20251215 (887e7ef) View Download
1 17 2kmt__assembly_1__model_17 dimeric （2） Success 4.1.3-1-20251215 (887e7ef) View Download
1 18 2kmt__assembly_1__model_18 dimeric （2） Success 4.1.3-1-20251215 (887e7ef) View Download
1 19 2kmt__assembly_1__model_19 dimeric （2） Success 4.1.3-1-20251215 (887e7ef) View Download
1 20 2kmt__assembly_1__model_20 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 (1)

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6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd2kmta_
Class classb — All beta proteins
Fold Fold foldb.34 — SH3-like barrel
Superfamily Superfamily superfamilyb.34.6 — Cell growth inhibitor/plasmid maintenance toxic component
Family Family familyb.34.6.1 — CcdB
Domain ID domain_idd2kmtb_
Class classb — All beta proteins
Fold Fold foldb.34 — SH3-like barrel
Superfamily Superfamily superfamilyb.34.6 — Cell growth inhibitor/plasmid maintenance toxic component
Family Family familyb.34.6.1 — CcdB

CATH v4.4 (2 domains)

Domain ID domain_id2kmtA00
Class class2 — Mainly Beta
Architecture architecture30 — Roll
Topology topology30 — SH3 type barrels.
Homologous superfamily homologous superfamily110 —
Domain ID domain_id2kmtB00
Class class2 — Mainly Beta
Architecture architecture30 — Roll
Topology topology30 — SH3 type barrels.
Homologous superfamily homologous superfamily110 —
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7. Citations (1)