4F4Y

Y-family DNA polymerase chimera Dbh-Dpo4-Dbh

Structural Biology Knowledgebase: 4F4Y SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.34 Å
  • R-Value Free: 0.259
  • R-Value Work: 0.222

Literature

Macromolecules
Sequence Display for 4F4Y

Classification: TRANSFERASE / DNA

Total Structure Weight: 104599.37


Macromolecule Entities
Molecule Chains Length Organism Details
DNA polymerase IV A, B 362 Sulfolobus acidocaldarius Sulfolobus solfataricus EC#: 2.7.7.7 IUBMB
Gene Name(s): dbh Saci_0554 dpo4 SSO2448
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Macromolecule Entities
Molecule Chains Length Organism Details
DNA (5'-D(*GP*GP*CP*AP*CP*TP*GP*AP*TP*CP*GP*GP*GP*CP*CP*C)-3') C, P 16 Synthetic construct Primer DNA
DNA (5'-D(*TP*TP*AP*CP*GP*CP*CP*CP*TP*GP*AP*TP*CP*AP*GP*TP*GP*CP*C)-3') D, T 19 Synthetic construct Template DNA

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

A, C 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE
C9 H16 N3 O13 P3
RGWHQCVHVJXOKC-SHYZEUOFSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CA
Query on CA

A, B CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.34 Å
  • R-Value Free: 0.259
  • R-Value Work: 0.222
  • Space Group: P 1 21 1

Unit Cell:

Length (Å) Angle (°)
a = 53.08 α = 90.00
b = 103.39 β = 101.76
c = 112.99 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2012-05-11
  • Released Date: 2013-01-02
  • Deposition author(s): Pata, J.D., Wilson, R.C.

Revision History

  • 2013-02-13
    Type: Citation | Details: Citation update