4JV0

Ring-Opening of the -OH-PdG Adduct in Ternary Complexes with the Sulfolobus solfataricus DNA polymerase Dpo4

Structural Biology Knowledgebase: 4JV0 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.95 Å
  • R-Value Free: 0.270
  • R-Value Work: 0.192

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 4JV0

Classification: TRANSFERASE / DNA

Total Structure Weight: 49357.07


Macromolecule Entities
Molecule Chains Length Organism Details
DNA polymerase IV A 347 Sulfolobus solfataricus EC#: 2.7.7.7 IUBMB
Gene Name(s): dbh dpo4 SSO2448
Macromolecule Entities
Molecule Chains Length Organism Details
DNA (5'-D(P*TP*(KAG)P*GP*AP*AP*TP*CP*CP*TP*TP*CP*CP*CP*CP*C)-3') B 15 synthetic
DNA (5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP*TP*TP*CP*C)-3') C 14 synthetic

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

A 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE
C10 H16 N5 O12 P3
SUYVUBYJARFZHO-RRKCRQDMSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CA
Query on CA

A CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
KAG
Query on KAG
B RNA LINKING C14 H20 N5 O8 P G

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.95 Å
  • R-Value Free: 0.270
  • R-Value Work: 0.192
  • Space Group: P 21 21 2
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 93.83 α = 90.00
b = 104.49 β = 90.00
c = 52.53 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2013-03-25
  • Released Date: 2013-08-28
  • Deposition author(s): Banerjee, S., Shanmugam, G., Stone, M.P.

Revision History

  • 2013-10-09
    Type: Citation | Details: Citation update