4DSJ

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

Structural Biology Knowledgebase: 4DSJ SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.86 Å
  • R-Value Free: 0.277
  • R-Value Work: 0.213

Literature

Macromolecules
Sequence Display for 4DSJ

Classification: TRANSFERASE / DNA

Total Structure Weight: 146209.16


Macromolecule Entities
Molecule Chains Length Organism Details
DNA polymerase A, B 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 C, E 12 synthetic
dGTP D, F 10 synthetic

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

A 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
HAAZLUGHYHWQIW-KVQBGUIXSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CA
Query on CA

A 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: 2.86 Å
  • R-Value Free: 0.277
  • R-Value Work: 0.213
  • Space Group: P 21 21 21

Unit Cell:

Length (Å) Angle (°)
a = 60.02 α = 90.00
b = 112.07 β = 90.00
c = 229.45 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