4DSL

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

Structural Biology Knowledgebase: 4DSL SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.286
  • R-Value Work: 0.222

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 4DSL

Classification: TRANSFERASE / DNA

Total Structure Weight: 75434.59


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(*G*GP*CP*TP*AP*CP*AP*GP*GP*AP*CP*TP*C)-3') B 13 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 1 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
SO4
Query on SO4

A SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.286
  • R-Value Work: 0.222
  • Space Group: P 21 21 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 88.34 α = 90.00
b = 93.59 β = 90.00
c = 104.62 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