4F2S

DNA Polymerase I Large Fragment complex 4

• PDB DOI: https://doi.org/10.2210/pdb4F2S/pdb
• NAKB: 4F2S

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


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

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 0.199 
• R-Value Work: 0.174 
• R-Value Observed: 0.175 

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: 150.17 kDa 
• Atom Count: 11,634 
• Modelled Residue Count: 1,202 
• 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*(DOC))-3')	C [auth B], E	9	synthetic construct

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

Oligosaccharides

Help

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose	G, H	2		N/A
Glycosylation Resources
GlyTouCan:  G05551OP GlyCosmos:  G05551OP

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CTP	I [auth A], J [auth D]	CYTIDINE-5'-TRIPHOSPHATE C9 H16 N3 O14 P3 PCDQPRRSZKQHHS-XVFCMESISA-N
SO4	L [auth D]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
MN	K [auth D]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 4
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900003	G, H	sucrose	Oligosaccharide / Nutrient

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 0.199 
• R-Value Work: 0.174 
• R-Value Observed: 0.175 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 93.18	α = 90
b = 108.59	β = 90
c = 150.99	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 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Structure summary
• Version 2.1: 2023-09-13
  Changes: Data collection, Database references, Refinement description, Structure summary