6K9A

The complex of NrS-1 N terminal domain (1-305) with dGTP

• PDB DOI: https://doi.org/10.2210/pdb6K9A/pdb

• Classification: TRANSFERASE
• Organism(s): Nitratiruptor phage NrS-1
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2019-06-14 Released: 2020-06-17 
• Deposition Author(s): Chen, X., Gan, J.
• Funding Organization(s): National Natural Science Foundation of China

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.248 
• R-Value Work: 0.209 
• R-Value Observed: 0.211 

Literature

Structural studies reveal a unique ring-shaped helicase architecture at the C-terminus of deep-sea vent phage DNA polymerase

Chen, X., Gan, J.

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: 35.45 kDa 
• Atom Count: 2,333 
• Modelled Residue Count: 279 
• Deposited Residue Count: 306 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Primase	A	306	Nitratiruptor phage NrS-1	Mutation(s): 0
UniProt
Find proteins for M5AAG8 (Nitratiruptor phage NrS-1) Explore M5AAG8  Go to UniProtKB:  M5AAG8

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DGT (Subject of Investigation/LOI)	D [auth A]	2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE C10 H16 N5 O13 P3 HAAZLUGHYHWQIW-KVQBGUIXSA-N
CA	B [auth A], C [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.248 
• R-Value Work: 0.209 
• R-Value Observed: 0.211 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 119.114	α = 90
b = 58.007	β = 92.96
c = 47.135	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-06-17 
Deposition Author(s): Chen, X., Gan, J.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China	China	31870721

Revision History  

• Version 1.0: 2020-06-17
  Type: Initial release
  
• Version 1.1: 2024-03-27
  Changes: Data collection, Database references