4K8X | pdb_00004k8x

Binary complex of 9N DNA polymerase in the replicative state

• PDB DOI: https://doi.org/10.2210/pdb4K8X/pdb
• NAKB: 4K8X

• Classification: TRANSFERASE/DNA
• Organism(s): Thermococcus sp. 9oN-7
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2013-04-19 Released: 2013-06-26 
• Deposition Author(s): Betz, K., Diederichs, K., Marx, A.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.28 Å
• R-Value Free: 
  0.238 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.195 (Depositor), 0.197 (DCC) 
• R-Value Observed: 
  0.198 (Depositor) 

Starting Model: experimental

Literature

Structures of KOD and 9N DNA Polymerases Complexed with Primer Template Duplex

Bergen, K., Betz, K., Welte, W., Diederichs, K., Marx, A.

(2013) Chembiochem 14: 1058-1062

• PubMed: 23733496 
• DOI: https://doi.org/10.1002/cbic.201300175
• Primary Citation Related Structures: 
  4K8X, 4K8Z


• PubMed Abstract: 
  

  Replicate it: Structures of KOD and 9°N DNA polymerases, two enzymes that are widely used to replicate DNA with highly modified nucleotides, were solved at high resolution in complex with primer/template duplex. The data elucidate substrate interaction of the two enzymes and pave the way for further optimisation of the enzymes and substrates.

---

Organizational Affiliation: 
• Department of Chemistry, Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstrasse 10, 78457 Konstanz, Germany.

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: 100.03 kDa 
• Atom Count: 7,110 
• Modeled Residue Count: 787 
• Deposited Residue Count: 803 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA polymerase	A	775	Thermococcus sp. 9oN-7	Mutation(s): 2  Gene Names: pol, polA EC: 2.7.7.7
UniProt
Find proteins for Q56366 (Thermococcus sp. (strain 9oN-7)) Explore Q56366  Go to UniProtKB:  Q56366

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*AP*AP*AP*GP*GP*CP*GP*CP*AP*GP*TP*TP*CP*GP*CP*G)-3')	B [auth T]	16	N/A

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*CP*GP*CP*GP*AP*AP*CP*TP*GP*CP*GP*(DOC))-3')	C [auth P]	12	N/A

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
5CY	P [auth T]	1-(3-hydroxypropyl)-2-{(1E,3E,5E)-5-[1-(3-hydroxypropyl)-3,3-dimethyl-1,3-dihydro-2H-indol-2-ylidene]penta-1,3-dien-1-y l}-3,3-dimethyl-3H-indolium C31 H39 N2 O2 VFBDPICHYNKCQJ-UHFFFAOYSA-N
SO4	D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], N [auth A], O [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
EDO	Q [auth T]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL	M [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.28 Å
• R-Value Free:  0.238 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.195 (Depositor), 0.197 (DCC) 
• R-Value Observed: 0.198 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 112.215	α = 90
b = 142.616	β = 90
c = 66.702	γ = 90

Software Package:

Software Name	Purpose
PHENIX	model building
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-06-26 
Deposition Author(s): Betz, K., Diederichs, K., Marx, A.

Revision History  

• Version 1.0: 2013-06-26
  Type: Initial release
  
• Version 1.1: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary
• Version 1.2: 2024-10-16
  Changes: Structure summary