6US5

DNA polymerase I Large Fragment from Bacillus stearothermophilus with DNA template, 3'-amino primer, dGpNHpp analog, and Mn2+


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.224 

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, 3'-amino primer, dGpNHpp analog, and Mn2+

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*(C42))-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
MN
Query on MN

Download SDF File 
Download CCD File 
A, D
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

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Download CCD File 
A, C, D
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
XG4
Query on XG4

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Download CCD File 
A, D
2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]guanosine
C10 H17 N6 O12 P3
DWGAAFQEGIMTIA-KVQBGUIXSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
C42
Query on C42
B, E
DNA LINKINGC9 H15 N4 O6 PDC
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.224 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 93.761α = 90.00
b = 108.805β = 90.00
c = 149.969γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
PHASERphasing
HKL-2000data scaling
HKL-2000data reduction

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