4ELT | pdb_00004elt

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

• PDB DOI: https://doi.org/10.2210/pdb4ELT/pdb
• NAKB: 4ELT

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


• Deposited: 2012-04-11 Released: 2013-03-27 
• Deposition Author(s): Marx, A., Diederichs, K., Obeid, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.209 (Depositor), 0.203 (DCC) 
• R-Value Work: 
  0.160 (Depositor), 0.155 (DCC) 
• R-Value Observed: 
  0.163 (Depositor) 

Starting Model: experimental

Literature

Interactions of non-polar and "Click-able" nucleotides in the confines of a DNA polymerase active site.

Obeid, S., Busskamp, H., Welte, W., Diederichs, K., Marx, A.

(2012) Chem Commun (Camb) 48: 8320-8322

• PubMed: 22766607 
• DOI: https://doi.org/10.1039/c2cc34181f
• Primary Citation Related Structures: 
  4ELT, 4ELU


• PubMed Abstract: 
  

  Modified nucleotides play a paramount role in many cutting-edge biomolecular techniques. The present structural study highlights the plasticity and flexibility of the active site of a DNA polymerase while incorporating non-polar "Click-able" nucleotide analogs and emphasizes new insights into rational design guidelines for modified nucleotides.

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Organizational Affiliation: 
• Department of Chemistry and Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstrasse 10, 78457 Konstanz, Germany.

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: 71.24 kDa 
• Atom Count: 5,231 
• Modeled Residue Count: 567 
• 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*(DOC))-3')	B	12	synthetic construct

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

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
0R5	D [auth A]	2'-deoxy-5-[(4-ethynylphenyl)ethynyl]uridine 5'-(tetrahydrogen triphosphate) C19 H19 N2 O14 P3 NDHYKBWELLKQHS-GVDBMIGSSA-N
GOL	G [auth A], I [auth A], J [auth A], L [auth A], M [auth A], N [auth A], P [auth A], R [auth B], S [auth C]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO	Q [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
ACT	H [auth A], K [auth A], O [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
MG	E [auth A], F [auth A], T [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.209 (Depositor), 0.203 (DCC) 
• R-Value Work:  0.160 (Depositor), 0.155 (DCC) 
• R-Value Observed: 0.163 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 108.86	α = 90
b = 108.86	β = 90
c = 91.004	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: 2013-03-27 
Deposition Author(s): Marx, A., Diederichs, K., Obeid, S.

Revision History  

• Version 1.0: 2013-03-27
  Type: Initial release
  
• Version 1.1: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description