4EZ9

Bacillus DNA Polymerase I Large Fragment Complex 2

• PDB DOI: https://doi.org/10.2210/pdb4EZ9/pdb
• NAKB: 4EZ9

• Classification: Transferase/DNA
• Organism(s): Geobacillus kaustophilus HTA426
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2012-05-02 Released: 2013-07-24 
• Deposition Author(s): Wang, W., Beese, L.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.64 Å
• R-Value Free: 0.191 
• R-Value Work: 0.168 
• R-Value Observed: 0.169 

Starting Model: experimental

Literature

Structures of a High-fidelity DNA Polymerase

Wang, W., Hellinga, H.W., Beese, L.S.

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)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 149.09 kDa 
• Atom Count: 11,567 
• Modelled Residue Count: 1,198 
• Deposited Residue Count: 1,228 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA polymerase	A, B [auth D]	592	Geobacillus kaustophilus HTA426	Mutation(s): 2  Gene Names: polA, GK2730 EC: 2.7.7.7
UniProt
Find proteins for Q5KWC1 (Geobacillus kaustophilus (strain HTA426)) Explore Q5KWC1  Go to UniProtKB:  Q5KWC1

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*CP*CP*TP*GP*AP*CP*TP*CP*(2DT))-3')	C [auth B], E	9	N/A

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*CP*AP*TP*TP*AP*GP*AP*GP*TP*CP*AP*GP*G)-3')	D [auth C], F	13	N/A

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
D3T	I [auth D]	2',3'-DIDEOXY-THYMIDINE-5'-TRIPHOSPHATE C10 H17 N2 O13 P3 URGJWIFLBWJRMF-JGVFFNPUSA-N
MPD	H [auth A]	(4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N
SO4	G [auth A], J [auth D]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.64 Å
• R-Value Free: 0.191 
• R-Value Work: 0.168 
• R-Value Observed: 0.169 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 93.92	α = 90
b = 108.96	β = 90
c = 149.49	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-07-24 
Deposition Author(s): Wang, W., Beese, L.S.

Revision History  

• Version 1.0: 2013-07-24
  Type: Initial release
  
• Version 1.1: 2015-02-04
  Changes: Other
• Version 1.2: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description