2OYQ

Crystal structure of RB69 gp43 in complex with DNA with 5-NIMP opposite an abasic site analog

Structural Biology Knowledgebase: 2OYQ SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.86 Å
  • R-Value Free: 0.294
  • R-Value Work: 0.228

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 2OYQ

Classification: transferase / DNA

Total Structure Weight: 464590.15


Macromolecule Entities
Molecule Chains Length Organism Details
DNA polymerase A, B, C, D 903 Enterobacteria phage rb69 EC#: 2.7.7.7 IUBMB 3.1.11 IUBMB
Mutation: D222A, D327A
Gene Name(s): 43
Macromolecule Entities
Molecule Chains Length Organism Details
Template DNA E, G, I, K 21 synthetic
Primer DNA F, H, J, L 15 synthetic

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

I, K MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer
 
JSmol
N5P
Query on N5P

A, C, I 1-{2-DEOXY-5-O-[(R)-HYDROXY{[(R)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]OXY}PHOSPHORYL]- BETA-D-ERYTHRO-PENTOFURANOSYL}-5-NITRO-1H- INDOLE
5-NITRO-1-INDOLYL-2'-DEOXYRIBOSIDE-5'-TRIPHOSPHATE (Synonym)
C13 H17 N2 O14 P3
JJJBDAFRCKSXDR-YNEHKIRRSA-N
Ligand Explorer
 
JSmol
Modified Residues 2 Unique
ID Chains Type Formula 2D Diagram Parent
3DR
Query on 3DR
E, G, I, K DNA LINKING C5 H11 O6 P --
N5I
Query on N5I
F, H, J, L DNA LINKING C13 H15 N2 O8 P --

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.86 Å
  • R-Value Free: 0.294
  • R-Value Work: 0.228
  • Space Group: P 1 21 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 132.59 α = 90.00
b = 123.48 β = 96.22
c = 164.33 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2007-02-22
  • Released Date: 2007-10-23
  • Deposition author(s): Zahn, K.E., Belrhali, H., Wallace, S.S., Doublie, S.

Revision History

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