4DTN

RB69 DNA Polymerase Ternary Complex with dATP Opposite an Abasic Site and ddA/dT as the Penultimate Base-pair

Structural Biology Knowledgebase: 4DTN SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.96 Å
  • R-Value Free: 0.216
  • R-Value Work: 0.184

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 4DTN

Classification: Transferase / DNA

Total Structure Weight: 114238.28


Macromolecule Entities
Molecule Chains Length Organism Details
DNA polymerase A 903 Enterobacteria phage rb69 EC#: 2.7.7.7 IUBMB 3.1.11 IUBMB
Mutation: D222A, D327A, L561A, S565G, Y567A
Gene Name(s): 43
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Macromolecule Entities
Molecule Chains Length Organism Details
DNA template T 17 synthetic
DNA primer P 13 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
3DR
Query on 3DR
T DNA LINKING C5 H11 O6 P --

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.96 Å
  • R-Value Free: 0.216
  • R-Value Work: 0.184
  • Space Group: P 21 21 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 78.28 α = 90.00
b = 118.13 β = 90.00
c = 130.22 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2012-02-21
  • Released Date: 2012-06-06
  • Deposition author(s): Xia, S., Wang, J., Konigsberg, W.H.

Revision History

  • 2012-09-05
    Type: Citation | Details: Citation update