6GDR

DNA binding with a minimal scaffold: Structure-function analysis of Lig E DNA ligases


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.33 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.218 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

DNA binding with a minimal scaffold: structure-function analysis of Lig E DNA ligases.

Williamson, A.Grgic, M.Leiros, H.S.

(2018) Nucleic Acids Res. --: --


Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
DNA ligase
A
297Alteromonas mediterraneaMutation(s): 0 
Find proteins for A0A1J0SCU0 (Alteromonas mediterranea)
Go to UniProtKB:  A0A1J0SCU0
Entity ID: 1
MoleculeChainsLengthOrganism
DNA (5'-D(*TP*TP*CP*CP*GP*AP*TP*AP*GP*TP*GP*GP*GP*GP*TP*CP*GP*CP*AP*AP*T)-3')B21Alteromonas mediterranea
Entity ID: 2
MoleculeChainsLengthOrganism
DNAC10Alteromonas mediterranea
Entity ID: 3
MoleculeChainsLengthOrganism
DNA (5'-D(P*CP*AP*CP*TP*AP*TP*CP*GP*GP*AP*A)-3')D11Alteromonas mediterranea
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download SDF File 
Download CCD File 
B
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
AMP
Query on AMP

Download SDF File 
Download CCD File 
D
ADENOSINE MONOPHOSPHATE
C10 H14 N5 O7 P
UDMBCSSLTHHNCD-KQYNXXCUSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.33 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.218 
  • Space Group: I 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 65.024α = 90.00
b = 71.207β = 94.82
c = 117.160γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Research Council of NorwayNorway244247

Revision History 

  • Version 1.0: 2018-07-25
    Type: Initial release