4DSI

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

Structural Biology Knowledgebase: 4DSI SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.234
  • R-Value Work: 0.191

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 4DSI

Classification: TRANSFERASE / DNA

Total Structure Weight: 73761.77


Macromolecule Entities
Molecule Chains Length Organism Details
DNA polymerase A 581 Geobacillus stearothermophilus EC#: 2.7.7.7 IUBMB
Fragment: RESIDUES 298-876
Mutation: A598D, P713V
Gene Name(s):
Macromolecule Entities
Molecule Chains Length Organism Details
DNA B 12 synthetic
Se-dGTP C 9 synthetic

Small Molecules
Ligands 4 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
DG
Query on DG

C 2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE
C10 H14 N5 O7 P
LTFMZDNNPPEQNG-KVQBGUIXSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SO4
Query on SO4

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

A GLYCEROL
2, (Synonym)
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CA
Query on CA

C CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.234
  • R-Value Work: 0.191
  • Space Group: P 21 21 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 88.57 α = 90.00
b = 93.39 β = 90.00
c = 105.93 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