4BDP

CRYSTAL STRUCTURE OF BACILLUS DNA POLYMERASE I FRAGMENT COMPLEXED TO 11 BASE PAIRS OF DUPLEX DNA AFTER ADDITION OF TWO DATP RESIDUES


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.296
  • R-Value Work: 0.248

Literature

Macromolecules
Sequence Display for 4BDP

Classification: TRANSFERASE / DNA

Total Structure Weight: 73861.48


Macromolecule Entities
Molecule Chains Length Organism Details
PROTEIN (DNA POLYMERASE I) A 580 Geobacillus stearothermophilus EC#: 2.7.7.7 IUBMB
Fragment: RESIDUES 297-876
Mutation: K298A, A411R, A456E, E505K, R512G, S550T, ΔQ576, R823H
Gene Name(s): polA pol
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Macromolecule Entities
Molecule Chains Length Organism Details
DNA (5'-D(*GP*CP*AP*TP*CP*AP*TP*GP*CP*AP*A)-3') P 11 synthetic
DNA (5'-D(*TP*AP*TP*TP*GP*CP*AP*TP*GP*AP*TP*GP*C)-3') T 13 synthetic

Small Molecules
Ligands 2 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
SO4
Query on SO4

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

A MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.296
  • R-Value Work: 0.248
  • Space Group: P 21 21 21

Unit Cell:

Length (Å) Angle (°)
a = 86.24 α = 90.00
b = 93.28 β = 90.00
c = 106.37 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 1997-11-17
  • Released Date: 1999-01-13
  • Deposition author(s): Kiefer, J.R., Mao, C., Beese, L.S.

Revision History

  • 2008-05-22
    Type: Version format compliance
  • 2011-07-13
    Type: Version format compliance