3C58

Crystal structure of a complex between the wild-type lactococcus lactis Fpg (MutM) and a N7-Benzyl-Fapy-dG containing DNA

Structural Biology Knowledgebase: 3C58 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.200
  • R-Value Work: 0.172

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 3C58

Classification: HYDROLASE / DNA

Total Structure Weight: 39939.82


Macromolecule Entities
Molecule Chains Length Organism Details
DNA glycosylase A 271 Lactococcus lactis EC#: 3.2.2.23 IUBMB
Gene Name(s): mutM fpg
Macromolecule Entities
Molecule Chains Length Organism Details
DNA (5'-D(*DGP*DCP*DGP*DAP*DGP*DAP*DAP*DAP*DCP*DAP*DAP*DAP*DGP*DA)-3') C 14 synthetic
DNA (5'-D(*DCP*DTP*DCP*DTP*DTP*DTP*(SOS)P*DTP*DTP*DTP*DCP*DTP*DCP*DG)-3') B 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
SOS
Query on SOS
B DNA LINKING C18 H24 N5 O7 P --

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.200
  • R-Value Work: 0.172
  • Space Group: P 41 21 2
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 91.36 α = 90.00
b = 91.36 β = 90.00
c = 140.94 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2008-01-31
  • Released Date: 2008-12-16
  • Deposition author(s): Coste, F., Castaing, B., Carell, T.

Revision History

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