3SJJ

RB69 DNA Polymerase Triple Mutant (L561A/S565G/Y567A) Ternary Complex with dUpNpp and a Deoxy-terminated Primer in the presence of Mn2+

Structural Biology Knowledgebase: 3SJJ SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.38 Å
  • R-Value Free: 0.265
  • R-Value Work: 0.202

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 3SJJ

Classification: TRANSFERASE / DNA

Total Structure Weight: 114792.71


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, D902A
Gene Name(s): 43
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Macromolecule Entities
Molecule Chains Length Organism Details
5'-D(*TP*CP*AP*AP*GP*TP*AP*AP*GP*CP*AP*GP*TP*CP*CP*GP*CP*G)-3' T 18 synthetic template DNA strand
5'-D(*GP*CP*GP*GP*AP*CP*TP*GP*CP*TP*TP*AP*C)-3' P 13 synthetic primer DNA strand

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

A 2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE
C9 H16 N3 O13 P3
XZLLMTSKYYYJLH-SHYZEUOFSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MN
Query on MN

A MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.38 Å
  • R-Value Free: 0.265
  • R-Value Work: 0.202
  • Space Group: P 21 21 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 78.56 α = 90.00
b = 118.22 β = 90.00
c = 130.11 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2011-06-21
  • Released Date: 2011-10-12
  • Deposition author(s): Wang, M., Wang, J., Konigsberg, W.H.

Revision History

  • 2011-11-02
    Type: Citation | Details: Citation update