3PX4

Crystal Structure of Bacillus DNA Polymerase I Large Fragment Bound to DNA and ddCTP-dA Mismatch (wobble) in Ajar Conformation


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.58 Å
  • R-Value Free: 0.239
  • R-Value Work: 0.211

Literature

Macromolecules
Sequence Display for 3PX4

Classification: TRANSFERASE / DNA

Total Structure Weight: 149452.13


Macromolecule Entities
Molecule Chains Length Organism Details
DNA polymerase I A, D 592 Geobacillus kaustophilus EC#: 2.7.7.7 IUBMB
Fragment: Bacillus Fragment (analogous to E. coli Klenow Fragment)
Mutation: D598A, F710Y, R823H
Gene Name(s): polA GK2730
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Macromolecule Entities
Molecule Chains Length Organism Details
DNA (5'-D(*CP*CP*TP*GP*AP*CP*TP*CP*(DOC))-3') B, E 9 synthetic
DNA (5'-D(*CP*AP*TP*AP*GP*GP*AP*GP*TP*CP*AP*GP*G)-3') C, F 13 synthetic

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

A, D 2',3'-DIDEOXYCYTIDINE 5'-TRIPHOSPHATE
C9 H16 N3 O12 P3
ARLKCWCREKRROD-POYBYMJQSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SO4
Query on SO4

D SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

D MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
DOC
Query on DOC
B, E DNA LINKING C9 H14 N3 O6 P DC

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.58 Å
  • R-Value Free: 0.239
  • R-Value Work: 0.211
  • Space Group: P 21 21 21

Unit Cell:

Length (Å) Angle (°)
a = 93.68 α = 90.00
b = 109.19 β = 90.00
c = 150.46 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2010-12-09
  • Released Date: 2011-10-19
  • Deposition author(s): Wang, W., Beese, L.S.

Revision History

  • Version 1_0: 2011-10-19

    Type: Initial release

  • Version 1_1: 2011-11-02

    Type: Database references

  • Version 1_2: 2011-11-09

    Type: Database references