6K9B | pdb_00006k9b

Apo structure of NrS-1 N terminal domain N305

• PDB DOI: https://doi.org/10.2210/pdb6K9B/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: 2.45 Å
• R-Value Free: 
  0.232 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.188 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.190 (Depositor) 

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.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 69.72 kDa 
• Atom Count: 4,476 
• Modeled Residue Count: 558 
• Deposited Residue Count: 612 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Primase	A, B	306	Nitratiruptor phage NrS-1	Mutation(s): 0  EC: 2.7.7.7 (UniProt), 3.6.4.12 (UniProt), 2.7.7 (UniProt)
UniProt
Find proteins for M5AAG8 (Nitratiruptor phage NrS-1) Explore M5AAG8  Go to UniProtKB:  M5AAG8

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.45 Å
• R-Value Free:  0.232 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.188 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.190 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.136	α = 90
b = 107.555	β = 113.34
c = 66.868	γ = 90

Software Package:

Software Name	Purpose
REFMAC	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, Refinement description