3OJU

Snapshot of the large fragment of DNA polymerase I from Thermus Aquaticus processing c5 modified thymidies

Structural Biology Knowledgebase: 3OJU SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.0 Å
  • R-Value Free: 0.219
  • R-Value Work: 0.177

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 3OJU

Classification: Transferase / DNA

Total Structure Weight: 72387.71


Macromolecule Entities
Molecule Chains Length Organism Details
DNA polymerase I, thermostable A 540 Thermus aquaticus EC#: 2.7.7.7 IUBMB
Fragment: unp residues 292-832
Gene Name(s): polA pol1
Macromolecule Entities
Molecule Chains Length Organism Details
DNA (5'-D(*GP*AP*CP*CP*AP*CP*GP*GP*CP*GP*CP*(DOC))-3') B 12 synthetic DNA PRIMER
DNA (5'-D(*AP*AP*AP*AP*GP*GP*CP*GP*CP*CP*GP*TP*GP*GP*TP*C)-3') C 16 synthetic DNA TEMPLATE

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

A 2'-deoxy-5-[(1-hydroxy-2,2,5,5-tetramethyl- 2,5-dihydro-1H-pyrrol-3-yl)ethynyl]uridine 5'- (tetrahydrogen triphosphate)
C19 H28 N3 O15 P3
GHJOELBEPYPBAG-RRFJBIMHSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
PGE
Query on PGE

A, C TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GOL
Query on GOL

A, C GLYCEROL
2, (Synonym)
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

A 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 DNA LINKING C9 H14 N3 O6 P DC

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.0 Å
  • R-Value Free: 0.219
  • R-Value Work: 0.177
  • Space Group: P 31 2 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 109.02 α = 90.00
b = 109.02 β = 90.00
c = 91.47 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2010-08-23
  • Released Date: 2010-12-15
  • Deposition author(s): Marx, A., Diederichs, K., Obeid, S.

Revision History

  • 2013-03-27
    Type: Citation | Details: Citation update
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4