4O0I | pdb_00004o0i

Crystal structure of fragment DNA polymerase I from Bacillus stearothermophilus with 2'-MeSe-arabino-guanosine derivatized DNA

• PDB DOI: https://doi.org/10.2210/pdb4O0I/pdb
• NAKB: 4O0I

• Classification: TRANSFERASE/DNA
• Organism(s): Geobacillus stearothermophilus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2013-12-13 Released: 2014-12-17 
• Deposition Author(s): Jiang, S., Gan, J., Sun, H., Huang, Z.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.228 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.176 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.179 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of fragment DNA polymerase I from Bacillus stearothermophilus with 2'-MeSe-arabino-guanosine derivatized DNA

Jiang, S., Gan, J., Sun, H., Huang, Z.

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)

Macromolecule Content 

• Total Structure Weight: 74.42 kDa 
• Atom Count: 5,386 
• Modeled Residue Count: 602 
• Deposited Residue Count: 604 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA polymerase I	A	580	Geobacillus stearothermophilus	Mutation(s): 0  Gene Names: DPO1 EC: 2.7.7.7
UniProt
Find proteins for D9N168 (Geobacillus stearothermophilus) Explore D9N168  Go to UniProtKB:  D9N168

Entity ID: 2
Molecule	Chains	Length	Organism	Image
5'-D(*C*(1TW)P*CP*GP*AP*AP*TP*TP*CP*GP*CP*G)-3'	B, C	12	N/A

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	J [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
NA	K [auth A], L [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.228 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.176 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.179 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 86.77	α = 90
b = 93.967	β = 90
c = 106.041	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-12-17 
Deposition Author(s): Jiang, S., Gan, J., Sun, H., Huang, Z.

Revision History  

• Version 1.0: 2014-12-17
  Type: Initial release
  
• Version 1.1: 2017-11-22
  Changes: Refinement description
• Version 1.2: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description