4ELV | pdb_00004elv

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

• PDB DOI: https://doi.org/10.2210/pdb4ELV/pdb
• NAKB: 4ELV

• Classification: TRANSFERASE/DNA
• Organism(s): Thermus aquaticus, synthetic construct
• Expression System: Escherichia coli
• Mutation(s): No 


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

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.216 (Depositor), 0.212 (DCC) 
• R-Value Work: 
  0.176 (Depositor), 0.174 (DCC) 
• R-Value Observed: 
  0.178 (Depositor) 

Starting Model: experimental

Literature

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

Obeid, S., Bu kamp, H., Welte, W., Diederichs, K., Marx, A.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 70.97 kDa 
• Atom Count: 5,242 
• Modeled Residue Count: 564 
• Deposited Residue Count: 568 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA polymerase I, thermostable	A	540	Thermus aquaticus	Mutation(s): 0  Gene Names: polA, pol1 EC: 2.7.7.7
UniProt
Find proteins for P19821 (Thermus aquaticus) Explore P19821  Go to UniProtKB:  P19821

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*GP*AP*CP*CP*AP*CP*GP*GP*CP*GP*CP*(0R8))-3')	B	12	synthetic construct

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*AP*AP*AP*GP*GP*GP*CP*GP*CP*CP*GP*TP*GP*GP*TP*C)-3')	C	16	synthetic construct

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
0R7	E [auth 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
PGE	G [auth A]	TRIETHYLENE GLYCOL C6 H14 O4 ZIBGPFATKBEMQZ-UHFFFAOYSA-N
GOL	F [auth A], H [auth A], I [auth A], M [auth C]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO	J [auth A], O [auth C]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
CA	K [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
MG	D [auth A], L [auth B], N [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.216 (Depositor), 0.212 (DCC) 
• R-Value Work:  0.176 (Depositor), 0.174 (DCC) 
• R-Value Observed: 0.178 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 109.213	α = 90
b = 109.213	β = 90
c = 91.047	γ = 120

Software Package:

Software Name	Purpose
XDS	data scaling
PHENIX	model building
PHENIX	refinement
XDS	data reduction
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

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

Revision History  

• Version 1.0: 2013-04-24
  Type: Initial release
  
• Version 1.1: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description