4ELV

Snapshot of the large fragment of DNA polymerase I from Thermus Aquaticus processing modified pyrimidines

Structural Biology Knowledgebase: 4ELV SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.216
  • R-Value Work: 0.176

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 4ELV

Classification: TRANSFERASE / DNA

Total Structure Weight: 70974.38


Macromolecule Entities
Molecule Chains Length Organism Details
DNA polymerase I, thermostable A 540 Thermus aquaticus EC#: 2.7.7.7 IUBMB
Fragment: UNP RESIDUES 293-832
Gene Name(s): polA pol1
Macromolecule Entities
Molecule Chains Length Organism Details
DNA (5'-D(*GP*AP*CP*CP*AP*CP*GP*GP*CP*GP*CP*(0R8))-3') B 12 Synthetic construct DNA primer
DNA (5'-D(*AP*AP*AP*GP*GP*GP*CP*GP*CP*CP*GP*TP*GP*GP*TP*C)-3') C 16 Synthetic construct DNA template

Small Molecules
Ligands 6 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
0R7
Query on 0R7

A [[(2S,5R)-5-[4-azanyl-5-[2-(4-ethynylphenyl)ethynyl]- 2-oxidanylidene-pyrimidin-1-yl]oxolan-2-yl]methoxy- oxidanyl-phosphoryl] phosphono hydrogen phosphate
C19 H20 N3 O12 P3
PROFTMDIPXHDEG-DLBZAZTESA-N
Ligand Explorer
 
JSmol
CA
Query on CA

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

A, C 1,2-ETHANEDIOL
ETHYLENE GLYCOL (Synonym)
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Ligand Explorer
 
JSmol
GOL
Query on GOL

A, C GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL (Synonym)
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Ligand Explorer
 
JSmol
MG
Query on MG

A, B, C MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer
 
JSmol
PGE
Query on PGE

A TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
Ligand Explorer
 
JSmol
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
0R8
Query on 0R8
B DNA LINKING C19 H18 N3 O6 P DC

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.216
  • R-Value Work: 0.176
  • Space Group: P 31 2 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 109.21 α = 90.00
b = 109.21 β = 90.00
c = 91.05 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2012-04-11
  • Released Date: 2013-04-24
  • Deposition author(s): Marx, A., Diederichs, K., Obeid, S.

Revision History

No revisions since initial release