4DSK

Crystal structure of fragment DNA polymerase I from Bacillus stearothermophilus with duplex DNA, PPi and Calcium

Structural Biology Knowledgebase: 4DSK SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.18 Å
  • R-Value Free: 0.243
  • R-Value Work: 0.185

Literature

Macromolecules
Sequence Display for 4DSK

Classification: TRANSFERASE / DNA

Total Structure Weight: 75907.96


Macromolecule Entities
Molecule Chains Length Organism Details
DNA polymerase A 579 Geobacillus stearothermophilus EC#: 2.7.7.7 IUBMB
Fragment: RESIDUES 298-876
Mutation: A598D, P713V
Gene Name(s):
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Macromolecule Entities
Molecule Chains Length Organism Details
DNA (5'-D(*GP*GP*CP*TP*AP*CP*AP*GP*GP*AP*CP*TP*CP*G)-3') B 14 synthetic
DNA (5'-D(*TP*CP*AP*CP*GP*AP*GP*TP*CP*CP*TP*GP*TP*AP*GP*CP*C)-3') C 17 synthetic

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

A PYROPHOSPHATE 2-
H2 O7 P2
XPPKVPWEQAFLFU-UHFFFAOYSA-L
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CA
Query on CA

A, B CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.18 Å
  • R-Value Free: 0.243
  • R-Value Work: 0.185
  • Space Group: P 21 21 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 86.69 α = 90.00
b = 93.34 β = 90.00
c = 106.36 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2012-02-19
  • Released Date: 2013-03-27
  • Deposition author(s): Gan, J.H., Abdur, R., Liu, H.H., Sheng, J., Caton-Willians, J., Soares, A.S., Huang, Z.

Revision History

No revisions since initial release