3HT3

Crystal structure of fragment DNA polymerase I from Bacillus stearothermophilus V713P mutant bound to G:dCTP

Structural Biology Knowledgebase: 3HT3 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.247
  • R-Value Work: 0.210

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 3HT3

Classification: TRANSFERASE / DNA

Total Structure Weight: 147654.47


Macromolecule Entities
Molecule Chains Length Organism Details
DNA polymerase I, large fragment A, D 579 Geobacillus stearothermophilus EC#: 2.7.7.7 IUBMB
Fragment: Residues 298-876
Mutation: D598A, V713P
Macromolecule Entities
Molecule Chains Length Organism Details
5'-D(*CP*GP*AP*TP*CP*AP*CP*GP*(DOC))-3' B, E 9 synthetic
5'-D(*AP*CP*GP*GP*CP*GP*TP*GP*AP*TP*CP*G)-3' C, F 12 synthetic

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

A, D 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE
C9 H16 N3 O13 P3
RGWHQCVHVJXOKC-SHYZEUOFSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SUC
Query on SUC

A, D SUCROSE
C12 H22 O11
CZMRCDWAGMRECN-UGDNZRGBSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SO4
Query on SO4

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

A, D MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
DOC
Query on DOC
B, E DNA LINKING C9 H14 N3 O6 P DC

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.247
  • R-Value Work: 0.210
  • Space Group: P 21 21 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 93.28 α = 90.00
b = 108.79 β = 90.00
c = 152.09 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2009-06-11
  • Released Date: 2010-07-14
  • Deposition author(s): Wu, E.Y., Beese, L.S.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4