4DSK

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


Experimental Data Snapshot

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

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Biochemical and structural insights into the fidelity of bacillus stearothermophilus DNA polymerase

Gan, J.H.Abdur, R.Liu, H.H.Sheng, J.Caton-Willians, J.Soares, A.S.Huang, Z.

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
DNA polymerase
A
579Geobacillus stearothermophilusEC: 2.7.7.7
Find proteins for E1C9K5 (Geobacillus stearothermophilus)
Go to UniProtKB:  E1C9K5
Entity ID: 1
MoleculeChainsLengthOrganism
DNA (5'-D(*GP*GP*CP*TP*AP*CP*AP*GP*GP*AP*CP*TP*CP*G)-3')B14N/A
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'-D(*TP*CP*AP*CP*GP*AP*GP*TP*CP*CP*TP*GP*TP*AP*GP*CP*C)-3')C17N/A
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
POP
Query on POP

Download SDF File 
Download CCD File 
A
PYROPHOSPHATE 2-
H2 O7 P2
XPPKVPWEQAFLFU-UHFFFAOYSA-L
 Ligand Interaction
CA
Query on CA

Download SDF File 
Download CCD File 
A, B
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
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
Unit Cell:
Length (Å)Angle (°)
a = 86.692α = 90.00
b = 93.339β = 90.00
c = 106.363γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data collection
PHASESphasing
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-03-27
    Type: Initial release