4F3O

DNA Polymerase I Large Fragment Complex 5


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.57 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.179 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Structures of a High-fidelity DNA Polymerase

Wang, W.Hellinga, H.W.Beese, L.S.

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA polymerase
A, D
592Geobacillus kaustophilus (strain HTA426)Gene Names: polA
EC: 2.7.7.7
Find proteins for Q5KWC1 (Geobacillus kaustophilus (strain HTA426))
Go to UniProtKB:  Q5KWC1
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'-D(*CP*CP*TP*GP*AP*CP*TP*CP*(2DT))-3')B,E9synthetic construct
Entity ID: 3
MoleculeChainsLengthOrganism
DNA (5'-D(*C*AP*TP*GP*AP*GP*AP*GP*TP*CP*AP*GP*G)-3')C,F13synthetic construct
Small Molecules
Ligands 4 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, D
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
D3T
Query on D3T

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Download CCD File 
D
2',3'-DIDEOXY-THYMIDINE-5'-TRIPHOSPHATE
C10 H17 N2 O13 P3
URGJWIFLBWJRMF-JGVFFNPUSA-N
 Ligand Interaction
MPD
Query on MPD

Download SDF File 
Download CCD File 
A
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
2DT
Query on 2DT
B, E
DNA LINKINGC10 H15 N2 O7 PDT
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.57 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.179 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 93.830α = 90.00
b = 109.330β = 90.00
c = 150.110γ = 90.00
Software Package:
Software NamePurpose
XSCALEdata scaling
XDSdata reduction
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2012-05-09 
  • Released Date: 2013-07-24 
  • Deposition Author(s): Wang, W., Beese, L.S.

Revision History 

  • Version 1.0: 2013-07-24
    Type: Initial release