1PJI

Crystal structure of wild type Lactococcus lactis FPG complexed to a 1,3 propanediol containing DNA

Structural Biology Knowledgebase: 1PJI SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.237
  • R-Value Work: 0.210

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 1PJI

Classification: Hydrolase / DNA

Total Structure Weight: 39918.79


Macromolecule Entities
Molecule Chains Length Organism Details
Formamidopyrimidine-DNA glycosylase A 271 Lactococcus lactis EC#: 3.2.2.23 IUBMB
Mutation: ΔD139
Gene Name(s): mutM fpg
Macromolecule Entities
Molecule Chains Length Organism Details
DNA (5'-D(*CP*TP*CP*TP*TP*TP*(PDI)P*TP*TP*TP*CP*TP*CP*G)-3') D 14 synthetic
DNA (5'-D(*GP*CP*GP*AP*GP*AP*AP*AP*CP*AP*AP*AP*GP*A)-3') E 14 synthetic

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

A GLYCEROL
2, (Synonym)
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ZN
Query on ZN

A ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
PDI
Query on PDI
D NON-POLYMER C3 H9 O5 P --

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.237
  • R-Value Work: 0.210
  • Space Group: P 41 21 2
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 91.96 α = 90.00
b = 91.96 β = 90.00
c = 142.08 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2003-06-03
  • Released Date: 2004-08-03
  • Deposition author(s): Pereira, K., Serre, L., Zelwer, C., Castaing, B.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4
  • 2011-07-13
    Type: Non-polymer description | Details: chemical name/synonym update