7OUE

Crystal structure of a trapped Pab-AGOG/single-standed DNA covalent intermediate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.04 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.178 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Crystal structure of a trapped Pab-AGOG/single-standed DNA covalent intermediate

Coste, F.Goffinont, S.Flament, D.Castaing, B.

To be published.

Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
N-glycosylase/DNA lyaseA, C, E, G242Pyrococcus abyssi GE5Mutation(s): 0 
Gene Names: PYRAB10170PAB1695
EC: 3.2.2 (PDB Primary Data), 4.2.99.18 (PDB Primary Data)
UniProt
Find proteins for Q9UZY0 (Pyrococcus abyssi (strain GE5 / Orsay))
Explore Q9UZY0 
Go to UniProtKB:  Q9UZY0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UZY0
Protein Feature View
Expand
  • Reference Sequence

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChainsLengthOrganismImage
DNA (5'-D(*TP*TP*TP*(PED)P*TP*TP*TP*CP*T)-3')B, D, F, H 9synthetic construct
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download Ideal Coordinates CCD File 
I [auth C],
K [auth G]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
K
Query on K

Download Ideal Coordinates CCD File 
J [auth E]POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.04 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.178 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 39.743α = 92.48
b = 74.259β = 100.74
c = 101.726γ = 105.46
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2022-06-22
    Type: Initial release