6DSY

Bst DNA polymerase I post-chemistry (n+1) structure

• PDB DOI: https://doi.org/10.2210/pdb6DSY/pdb
• NAKB: 6DSY

• Classification: Transferase/DNA
• Organism(s): synthetic construct, Geobacillus stearothermophilus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2018-06-14 Released: 2018-10-31 
• Deposition Author(s): Chim, N., Jackson, L.N., Chaput, J.C.
• Funding Organization(s): National Science Foundation (NSF, United States)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.98 Å
• R-Value Free: 0.255 
• R-Value Work: 0.203 
• R-Value Observed: 0.204 

Starting Model: experimental

Literature

Crystal structures of DNA polymerase I capture novel intermediates in the DNA synthesis pathway.

Chim, N., Jackson, L.N., Trinh, A.M., Chaput, J.C.

(2018) Elife 7

• PubMed: 30338759 
• DOI: https://doi.org/10.7554/eLife.40444
• Primary Citation of Related Structures:  
  6DSU, 6DSV, 6DSW, 6DSX, 6DSY


• PubMed Abstract: 
  

  High resolution crystal structures of DNA polymerase intermediates are needed to study the mechanism of DNA synthesis in cells. Here we report five crystal structures of DNA polymerase I that capture new conformations for the polymerase translocation and nucleotide pre-insertion steps in the DNA synthesis pathway. We suggest that these new structures, along with previously solved structures, highlight the dynamic nature of the finger subdomain in the enzyme active site.

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Organizational Affiliation: 

Departments of Pharmaceutical Sciences, University of California, Irvine, California.

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: 73.7 kDa 
• Atom Count: 5,645 
• Modelled Residue Count: 600 
• Deposited Residue Count: 604 
• 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  Gene Names: polA EC: 2.7.7.7
UniProt
Find proteins for E1C9K5 (Geobacillus stearothermophilus) Explore E1C9K5  Go to UniProtKB:  E1C9K5

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*GP*CP*GP*AP*TP*CP*AP*CP*GP*T)-3')	A [auth P]	11	synthetic construct

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*GP*TP*AP*CP*GP*TP*GP*AP*TP*CP*GP*CP*A)-3')	B [auth T]	13	synthetic construct

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.98 Å
• R-Value Free: 0.255 
• R-Value Work: 0.203 
• R-Value Observed: 0.204 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 88.199	α = 90
b = 93.751	β = 90
c = 105.846	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
autoXDS	data reduction
autoXDS	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2018-10-31 
Deposition Author(s): Chim, N., Jackson, L.N., Chaput, J.C.

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Funding Organization	Location	Grant Number
National Science Foundation (NSF, United States)	United States	MCB: 1607111

Revision History  

• Version 1.0: 2018-10-31
  Type: Initial release
  
• Version 1.1: 2019-11-27
  Changes: Author supporting evidence
• Version 1.2: 2023-10-11
  Changes: Data collection, Database references, Refinement description