1DDN

DIPHTHERIA TOX REPRESSOR (C102D MUTANT)/TOX DNA OPERATOR COMPLEX

Structural Biology Knowledgebase: 1DDN SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.0 Å
  • R-Value Free: 0.280
  • R-Value Work: 0.240

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 1DDN

Classification: GENE REGULATION / DNA

Total Structure Weight: 122207.60


Macromolecule Entities
Molecule Chains Length Organism Details
DIPHTHERIA TOX REPRESSOR A, B, C, D 226 Corynebacterium diphtheriae Mutation: C102D
Gene Name(s): dtxR DIP1414
Macromolecule Entities
Molecule Chains Length Organism Details
33 BASE DNA CONTAINING TOXIN OPERATOR E 33 synthetic
33 BASE DNA CONTAINING TOXIN OPERATOR F 33 synthetic

Small Molecules
Ligands 1 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
NI
Query on NI

A, B, C, D NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.0 Å
  • R-Value Free: 0.280
  • R-Value Work: 0.240
  • Space Group: P 41

Unit Cell:

Length (Å) Angle (°)
a = 117.05 α = 90.00
b = 117.05 β = 90.00
c = 145.34 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 1998-06-23
  • Released Date: 1998-10-14
  • Deposition author(s): White, A., Ding, X., Vanderspek, J.C., Murphy, J.R., Ringe, D.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4