3PV8

Crystal Structure of Bacillus DNA Polymerase I Large Fragment Bound to DNA and ddTTP-dA in Closed Conformation

Structural Biology Knowledgebase: 3PV8 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.52 Å
  • R-Value Free: 0.211
  • R-Value Work: 0.185

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 3PV8

Classification: TRANSFERASE / DNA

Total Structure Weight: 149602.05


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*(2DT))-3') B, E 9 synthetic
DNA (5'-D(*C*AP*TP*AP*AP*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
D3T
Query on D3T

A, D 2',3'-DIDEOXY-THYMIDINE-5'-TRIPHOSPHATE
C10 H17 N2 O13 P3
URGJWIFLBWJRMF-JGVFFNPUSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SO4
Query on SO4

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

A, D MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
2DT
Query on 2DT
B, E DNA LINKING C10 H15 N2 O7 P DT

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.52 Å
  • R-Value Free: 0.211
  • R-Value Work: 0.185
  • Space Group: P 21 21 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 93.89 α = 90.00
b = 109.30 β = 90.00
c = 150.42 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2010-12-06
  • Released Date: 2011-10-19
  • Deposition author(s): Wang, W., Beese, L.S.

Revision History

  • 2011-11-09
    Type: Citation | Details: Citation update
  • 2011-11-02
    Type: Citation | Details: Citation update