6UR9

DNA polymerase I Large Fragment from Bacillus stearothermophilus with DNA template, dideoxy primer, 3'-amino-ddGTP (nGTP), and Ca2+


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.204 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

DNA polymerase I Large Fragment from Bacillus stearothermophilus with DNA template, dideoxy primer, 3'-amino-ddGTP (nGTP), and Ca2+

Lelyveld, V.S.Zhang, W.Szostak, J.W.

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA polymerase I
A, D
579Geobacillus stearothermophilusMutation(s): 1 
Gene Names: DPO1 (polA)
EC: 2.7.7.7
Find proteins for D9N168 (Geobacillus stearothermophilus)
Go to UniProtKB:  D9N168
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'-D(*GP*CP*GP*AP*TP*CP*AP*GP*(DOC))-3')B,E9synthetic construct
Entity ID: 3
MoleculeChainsLengthOrganism
DNA (5'-D(*CP*AP*CP*GP*CP*TP*GP*AP*TP*CP*GP*CP*A)-3')C,F13synthetic construct
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, D
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
CA
Query on CA

Download SDF File 
Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
NG3
Query on NG3

Download SDF File 
Download CCD File 
A
3'-amino-2',3'-dideoxyguanosine 5'-(tetrahydrogen triphosphate)
3'-amino-dGTP
C10 H17 N6 O12 P3
ILTYANYMUGEMNF-KVQBGUIXSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
DOC
Query on DOC
B, E
DNA LINKINGC9 H14 N3 O6 PDC
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.204 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 93.629α = 90.00
b = 108.069β = 90.00
c = 149.748γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
PHASERphasing
PDB_EXTRACTdata extraction
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Howard Hughes Medical Institute (HHMI)United States--

Revision History 

  • Version 1.0: 2020-03-18
    Type: Initial release