7RR4 | pdb_00007rr4

Structure of Deep-Sea Phage NrS-1 Primase-Polymerase N300 in complex with magnesium and pyrophosphate

• PDB DOI: https://doi.org/10.2210/pdb7RR4/pdb

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


• Deposited: 2021-08-09 Released: 2022-01-12 
• Deposition Author(s): Wang, L., Yu, C., Sliz, P.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.86 Å
• R-Value Free: 
  0.232 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.216 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.217 (Depositor) 

Starting Model: experimental

Literature

Molecular Dissection of the Primase and Polymerase Activities of Deep-Sea Phage NrS-1 Primase-Polymerase

Huang, F., Lu, X., Yu, C., Sliz, P., Wang, L., Zhu, B.

(2021) Frontiers In Microbiology 12: 766612

• DOI: https://doi.org/10.3389/fmicb.2021.766612

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: 32.78 kDa 
• Atom Count: 2,228 
• Modeled Residue Count: 273 
• Deposited Residue Count: 288 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Primase	A	288	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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PPV (Subject of Investigation/LOI)	D [auth A]	PYROPHOSPHATE H4 O7 P2 XPPKVPWEQAFLFU-UHFFFAOYSA-N
MG	B [auth A], C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.86 Å
• R-Value Free:  0.232 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.216 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.217 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 119.34	α = 90
b = 56.903	β = 93.602
c = 48.564	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
xia2	data reduction
xia2	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-01-12 
Deposition Author(s): Wang, L., Yu, C., Sliz, P.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2022-01-12
  Type: Initial release
  
• Version 1.1: 2023-10-18
  Changes: Data collection, Refinement description