1Q9Y

CRYSTAL STRUCTURE OF ENTEROBACTERIA PHAGE RB69 GP43 DNA POLYMERASE COMPLEXED WITH 8-OXOGUANOSINE CONTAINING DNA

Structural Biology Knowledgebase: 1Q9Y SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.271
  • R-Value Work: 0.204

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 1Q9Y

Classification: TRANSFERASE REPLICATION / DNA

Total Structure Weight: 115348.85


Macromolecule Entities
Molecule Chains Length Organism Details
DNA POLYMERASE A 906 Enterobacteria phage rb69 EC#: 2.7.7.7 IUBMB 3.1.11 IUBMB
Mutation: D225A, D330A
Gene Name(s): 43
Macromolecule Entities
Molecule Chains Length Organism Details
5'-AC(8-OXOGUANOSINE)GGTAAGCAGTCCGCG-3' T 18 synthetic
5'-GCGGACTGCTTAC(DIDEOXYCYTIDINE)-3' P 14 synthetic

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

A CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Ligand Explorer
 
JSmol
DCP
Query on DCP

P 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE
C9 H16 N3 O13 P3
RGWHQCVHVJXOKC-SHYZEUOFSA-N
Ligand Explorer
 
JSmol
Modified Residues 2 Unique
ID Chains Type Formula 2D Diagram Parent
8OG
Query on 8OG
T DNA LINKING C10 H14 N5 O8 P DG
DOC
Query on DOC
P DNA LINKING C9 H14 N3 O6 P DC

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.271
  • R-Value Work: 0.204
  • Space Group: P 21 21 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 80.82 α = 90.00
b = 118.57 β = 90.00
c = 127.22 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2003-08-26
  • Released Date: 2004-04-27
  • Deposition author(s): Freisinger, E., Grollman, A.P., Miller, H., Kisker, C.

Revision History

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