6M3L

Crystal structure of the R.PabI(Y68F-K154A)-dsDNA(nonspecific) complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 0.306 
  • R-Value Work: 0.283 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Distortion of double-stranded DNA structure by the binding of the restriction DNA glycosylase R.PabI

Miyazono, K.Wang, D.Ito, T.Tanokura, M.

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
RE_R_Pab1 domain-containing protein
A, B
220Pyrococcus abyssi (strain GE5 / Orsay)Mutation(s): 2 
Find proteins for G8ZFZ3 (Pyrococcus abyssi (strain GE5 / Orsay))
Go to UniProtKB:  G8ZFZ3
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'-D(*CP*GP*CP*AP*TP*CP*GP*AP*TP*TP*CP*AP*GP*AP*AP*TP*CP*GP*AP*TP*GP*CP*G)-3')C23synthetic construct
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 0.306 
  • R-Value Work: 0.283 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 84.153α = 90.00
b = 84.153β = 90.00
c = 140.530γ = 120.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
MOLREPphasing
XDSdata reduction
PHENIXrefinement
XDSdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2020-03-18
    Type: Initial release
  • Version 1.1: 2020-04-01
    Type: Derived calculations