4DTO

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

Structural Biology Knowledgebase: 4DTO SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.225
  • R-Value Work: 0.185

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 4DTO

Classification: Transferase / DNA

Total Structure Weight: 114214.52


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
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
CA
Query on CA

A CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Ligand Explorer
 
JSmol
DCP
Query on DCP

A 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE
C9 H16 N3 O13 P3
RGWHQCVHVJXOKC-SHYZEUOFSA-N
Ligand Explorer
 
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: 2.05 Å
  • R-Value Free: 0.225
  • R-Value Work: 0.185
  • Space Group: P 21 21 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 78.24 α = 90.00
b = 119.26 β = 90.00
c = 130.92 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