4K8Z | pdb_00004k8z

KOD Polymerase in binary complex with dsDNA

• PDB DOI: https://doi.org/10.2210/pdb4K8Z/pdb
• NAKB: 4K8Z

• Classification: TRANSFERASE/DNA
• Organism(s): Thermococcus kodakarensis KOD1
• Expression System: Escherichia coli
• Mutation(s): Yes 


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

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.29 Å
• R-Value Free: 
  0.218 (Depositor), 0.221 (DCC) 
• R-Value Work: 
  0.181 (Depositor), 0.185 (DCC) 
• R-Value Observed: 
  0.183 (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.

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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: 98.92 kDa 
• Atom Count: 7,141 
• Modeled Residue Count: 782 
• Deposited Residue Count: 802 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA polymerase	A	774	Thermococcus kodakarensis KOD1	Mutation(s): 2  Gene Names: pol, pol TK0001, TK0001 EC: 2.7.7.7
UniProt
Find proteins for P77933 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1)) Explore P77933  Go to UniProtKB:  P77933

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*AP*AP*AP*TP*TP*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*(2DA))-3')	C [auth P]	12	N/A

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NCO	D [auth A]	COBALT HEXAMMINE(III) Co H18 N6 DYLMFCCYOUSRTK-UHFFFAOYSA-N
EDO	E [auth A], F [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
MG	G [auth T]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.29 Å
• R-Value Free:  0.218 (Depositor), 0.221 (DCC) 
• R-Value Work:  0.181 (Depositor), 0.185 (DCC) 
• R-Value Observed: 0.183 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 144.87	α = 90
b = 111.78	β = 90
c = 67.1	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

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

Revision History  

• Version 1.0: 2013-06-26
  Type: Initial release
  
• Version 1.1: 2017-08-09
  Changes: Refinement description, Source and taxonomy
• Version 1.2: 2017-11-15
  Changes: Refinement description
• Version 1.3: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.4: 2024-10-30
  Changes: Structure summary