1L3V

Crystal Structure of Bacillus DNA Polymerase I Fragment product complex with 15 base pairs of duplex DNA following addition of dTTP, dATP, dCTP, and dGTP residues.

• PDB DOI: https://doi.org/10.2210/pdb1L3V/pdb
• NAKB: 1L3V

• Classification: TRANSFERASE/DNA
• Organism(s): Geobacillus stearothermophilus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2002-03-01 Released: 2003-03-25 
• Deposition Author(s): Johnson, S.J., Taylor, J.S., Beese, L.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.71 Å
• R-Value Free: 0.234 
• R-Value Work: 0.206 
• R-Value Observed: 0.207 

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 76.66 kDa 
• Atom Count: 5,849 
• Modelled Residue Count: 611 
• Deposited Residue Count: 611 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA Polymerase I	C [auth A]	580	Geobacillus stearothermophilus	Mutation(s): 0  EC: 2.7.7.7
UniProt
Find proteins for P52026 (Geobacillus stearothermophilus) Explore P52026  Go to UniProtKB:  P52026

Entity ID: 1
Molecule	Chains	Length	Organism	Image
5'-D(*GP*CP*GP*AP*TP*CP*AP*CP*GP*TP*AP*CP*GP*TP*C)-3'	A [auth B]	15	N/A

Entity ID: 2
Molecule	Chains	Length	Organism	Image
5'-D(*GP*AP*CP*GP*TP*AP*CP*GP*TP*GP*AP*TP*CP*GP*CP*A)-3'	B [auth C]	16	N/A

Oligosaccharides

Help

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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	F [auth A], G [auth A], H [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
MG	I [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Biologically Interesting Molecules (External Reference) 1 Unique

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.71 Å
• R-Value Free: 0.234 
• R-Value Work: 0.206 
• R-Value Observed: 0.207 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 88.072	α = 90
b = 93.378	β = 90
c = 104.919	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
CNS	refinement
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2003-03-25 
Deposition Author(s): Johnson, S.J., Taylor, J.S., Beese, L.S.

Revision History  

• Version 1.0: 2003-03-25
  Type: Initial release
  
• Version 1.1: 2008-04-28
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
• Version 2.1: 2023-08-16
  Changes: Data collection, Database references, Refinement description, Structure summary