4E0D

Binary complex of Bacillus DNA Polymerase I Large Fragment E658A and duplex DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.58 Å
  • R-Value Free: 0.181
  • R-Value Work: 0.161

Literature

Macromolecules
Sequence Display for 4E0D

Classification: TRANSFERASE / DNA

Total Structure Weight: 75605.88


Macromolecule Entities
Molecule Chains Length Organism Details
DNA polymerase A 592 Geobacillus kaustophilus EC#: 2.7.7.7 IUBMB
Fragment: Bacillus Fragment (analogous to E. coli Klenow Fragment)
Mutation: D598A, E658A, R823H
Gene Name(s): polA GK2730
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Macromolecule Entities
Molecule Chains Length Organism Details
DNA (5'-D(*CP*CP*TP*GP*AP*CP*TP*CP*(DOC))-3') B 9 Synthetic construct Primer Strand
DNA (5'-D(*CP*AP*TP*GP*GP*GP*AP*GP*TP*CP*AP*GP*G)-3') C 13 Synthetic construct Template Strand

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

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

A 2-(N-MORPHOLINO)-ETHANESULFONIC ACID
C6 H13 N O4 S
SXGZJKUKBWWHRA-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MPD
Query on MPD

A (4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SO4
Query on SO4

A SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Ligand Explorer NGL
 
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: 1.58 Å
  • R-Value Free: 0.181
  • R-Value Work: 0.161
  • Space Group: P 21 21 21

Unit Cell:

Length (Å) Angle (°)
a = 87.86 α = 90.00
b = 93.78 β = 90.00
c = 104.87 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2012-03-02
  • Released Date: 2012-06-06
  • Deposition author(s): Wang, W., Beese, L.S.

Revision History

  • Version 1_0: 2012-06-06

    Type: Initial release

  • Version 1_1: 2012-06-13

    Type: Database references

  • Version 1_2: 2012-09-05

    Type: Database references