1DIZ

CRYSTAL STRUCTURE OF E. COLI 3-METHYLADENINE DNA GLYCOSYLASE (ALKA) COMPLEXED WITH DNA

Structural Biology Knowledgebase: 1DIZ SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.290
  • R-Value Work: 0.250

Literature

Macromolecules
Sequence Display for 1DIZ

Classification: HYDROLASE / DNA

Total Structure Weight: 78531.27


Macromolecule Entities
Molecule Chains Length Organism Details
3-METHYLADENINE DNA GLYCOSYLASE II A, B 282 Escherichia coli EC#: 3.2.2.21 IUBMB
Gene Name(s): alkA aidA b2068 JW2053
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Macromolecule Entities
Molecule Chains Length Organism Details
DNA (5'-D(*GP*AP*CP*AP*TP*GP*AP*(NRI)P*TP*GP*CP*CP*T)-3') C, E 13 Escherichia coli
DNA (5'-D(*GP*GP*CP*AP*AP*TP*CP*AP*TP*GP*TP*CP*A)-3') D, F 13 Escherichia coli

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

A, B SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
NRI
Query on NRI
C, E DNA LINKING C5 H12 N O5 P --

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.290
  • R-Value Work: 0.250
  • Space Group: P 31 2 1

Unit Cell:

Length (Å) Angle (°)
a = 82.40 α = 90.00
b = 82.40 β = 90.00
c = 199.70 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 1999-11-30
  • Released Date: 2000-03-20
  • Deposition author(s): Hollis, T., Ichikawa, Y., Ellenberger, T.E.

Revision History

  • 2016-04-27
    Type: Linkage | Details: --
  • 2016-04-27
    Type: Source and taxonomy | Details: --
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4