4F2R

DNA Polymerase I Large Fragment complex 3

Structural Biology Knowledgebase: 4F2R SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.63 Å
  • R-Value Free: 0.192
  • R-Value Work: 0.170

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 4F2R

Classification: Transferase / DNA

Total Structure Weight: 150330.28


Macromolecule Entities
Molecule Chains Length Organism Details
DNA polymerase A, D 592 Geobacillus kaustophilus EC#: 2.7.7.7 IUBMB
Fragment: unp residues 287-878
Mutation: D598A, F710Y, R823H
Gene Name(s): polA GK2730
Macromolecule Entities
Molecule Chains Length Organism Details
DNA (5'-D(*CP*CP*TP*GP*AP*CP*TP*CP*(DOC))-3') B, E 9 Synthetic construct DNA Primer Strand
DNA (5'-D(*CP*AP*TP*GP*GP*GP*AP*GP*TP*CP*AP*GP*G)-3') C, F 13 Synthetic construct DNA Template Strand

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

A, D CYTIDINE-5'-TRIPHOSPHATE
C9 H16 N3 O14 P3
PCDQPRRSZKQHHS-XVFCMESISA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SUC
Query on SUC

A, D SUCROSE
C12 H22 O11
CZMRCDWAGMRECN-UGDNZRGBSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SO4
Query on SO4

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

D 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, E DNA LINKING C9 H14 N3 O6 P DC

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.63 Å
  • R-Value Free: 0.192
  • R-Value Work: 0.170
  • Space Group: P 21 21 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 93.22 α = 90.00
b = 108.48 β = 90.00
c = 150.95 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2012-05-08
  • Released Date: 2013-07-24
  • Deposition author(s): Wang, W., Beese, L.S.

Revision History

No revisions since initial release