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1f5t

DIPHTHERIA TOX REPRESSOR (C102D MUTANT) COMPLEXED WITH NICKEL AND DTXR CONSENSUS BINDING SEQUENCE

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

DIPHTHERIA TOXIN REPRESSOR

Corynebacterium diphtheriae

UniProt P33120

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein–DNA Homooligomer Protein 4 DNA 2 43MER DNA CONTAINING DXTR CONSENSUS BINDING SEQUENCE × 1 43MER DNA CONTAINING DXTR CONSENSUS BINDING SEQUENCE × 1 NICKEL (II) ION × 8 water × 4 Consistent with all polymers

Other States of the Same Protein in the Database

Monomer
1bi0 1bi1 1bym 1p92 1qvp 1qw1

6 assemblies

Homodimer
1bi2 1bi3 1dpr 1fwz 1g3s 1g3t 1g3w 1g3y 1p92 1xcv 2dtr 2qq9

16 assemblies; showing the first 12

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
1c0w 1ddn 1f5t

3 assemblies

View Construct and Data Evidence
UniProt name DTXR_CORDI
Isoform —
PDB entities 3
Chains and sequence ranges Author chain A； PDBConstruct 1–121； UniProt 1–121 Author chain B； PDBConstruct 1–121； UniProt 1–121 Author chain C； PDBConstruct 1–121； UniProt 1–121 Author chain D； PDBConstruct 1–121； UniProt 1–121

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_id1f5t
Deposition date deposition_date2000-06-15
Structure title titleDIPHTHERIA TOX REPRESSOR (C102D MUTANT) COMPLEXED WITH NICKEL AND DTXR CONSENSUS BINDING SEQUENCE
Keywords keywords;iron-regulated repressor, DNA-protein complex, helix-turn-helix motif, transcription regulator, diphtheria tox repressor, DNA-binding regulatory protein, TRANSCRIPTION-DNA COMPLEX ;; TRANSCRIPTION/DNA
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.

1f5t__assembly_1__model_1

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

Download this curve (.dat)

1f5t__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.

1f5t__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）35.67 Å
Rg (electron density)34.82 Å
Total Rg35.16 Å
Atom count5617
Residues566
Excluded volume94386 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 1f5t__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 (5)

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6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

Domain ID domain_idd1f5ta1
Class classa — All alpha proteins
Fold Fold folda.4 — DNA/RNA-binding 3-helical bundle
Superfamily Superfamily superfamilya.4.5 — 'Winged helix' DNA-binding domain
Family Family familya.4.5.24 — Iron-dependent repressor protein
Domain ID domain_idd1f5ta2
Class classa — All alpha proteins
Fold Fold folda.76 — Iron-dependent repressor protein, dimerization domain
Superfamily Superfamily superfamilya.76.1 — Iron-dependent repressor protein, dimerization domain
Family Family familya.76.1.1 — Iron-dependent repressor protein, dimerization domain
Domain ID domain_idd1f5tb1
Class classa — All alpha proteins
Fold Fold folda.4 — DNA/RNA-binding 3-helical bundle
Superfamily Superfamily superfamilya.4.5 — 'Winged helix' DNA-binding domain
Family Family familya.4.5.24 — Iron-dependent repressor protein
Domain ID domain_idd1f5tb2
Class classa — All alpha proteins
Fold Fold folda.76 — Iron-dependent repressor protein, dimerization domain
Superfamily Superfamily superfamilya.76.1 — Iron-dependent repressor protein, dimerization domain
Family Family familya.76.1.1 — Iron-dependent repressor protein, dimerization domain
Domain ID domain_idd1f5tc1
Class classa — All alpha proteins
Fold Fold folda.4 — DNA/RNA-binding 3-helical bundle
Superfamily Superfamily superfamilya.4.5 — 'Winged helix' DNA-binding domain
Family Family familya.4.5.24 — Iron-dependent repressor protein
Domain ID domain_idd1f5tc2
Class classa — All alpha proteins
Fold Fold folda.76 — Iron-dependent repressor protein, dimerization domain
Superfamily Superfamily superfamilya.76.1 — Iron-dependent repressor protein, dimerization domain
Family Family familya.76.1.1 — Iron-dependent repressor protein, dimerization domain
Domain ID domain_idd1f5td1
Class classa — All alpha proteins
Fold Fold folda.4 — DNA/RNA-binding 3-helical bundle
Superfamily Superfamily superfamilya.4.5 — 'Winged helix' DNA-binding domain
Family Family familya.4.5.24 — Iron-dependent repressor protein
Domain ID domain_idd1f5td2
Class classa — All alpha proteins
Fold Fold folda.76 — Iron-dependent repressor protein, dimerization domain
Superfamily Superfamily superfamilya.76.1 — Iron-dependent repressor protein, dimerization domain
Family Family familya.76.1.1 — Iron-dependent repressor protein, dimerization domain

CATH v4.4 (8 domains)

Domain ID domain_id1f5tA01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily10 — Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain
Domain ID domain_id1f5tA02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology60 — Diphtheria Toxin Repressor; domain 2
Homologous superfamily homologous superfamily10 — Iron dependent repressor, metal binding and dimerisation domain
Domain ID domain_id1f5tB01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily10 — Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain
Domain ID domain_id1f5tB02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology60 — Diphtheria Toxin Repressor; domain 2
Homologous superfamily homologous superfamily10 — Iron dependent repressor, metal binding and dimerisation domain
Domain ID domain_id1f5tC01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily10 — Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain
Domain ID domain_id1f5tC02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology60 — Diphtheria Toxin Repressor; domain 2
Homologous superfamily homologous superfamily10 — Iron dependent repressor, metal binding and dimerisation domain
Domain ID domain_id1f5tD01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily10 — Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain
Domain ID domain_id1f5tD02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology60 — Diphtheria Toxin Repressor; domain 2
Homologous superfamily homologous superfamily10 — Iron dependent repressor, metal binding and dimerisation domain
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7. Citations (1)