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

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.86 Å
R-Value Free:
0.232 (Depositor), 0.249 (DCC)
R-Value Work:
0.216 (Depositor)
R-Value Observed:
0.217 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

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

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

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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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	M5AAG8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PPV (Subject of Investigation/LOI) Query on PPV Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	PYROPHOSPHATE H₄ O₇ P₂ XPPKVPWEQAFLFU-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain B [auth A] MOL2 format, chain C [auth A] MOL2 format, chain B [auth A] mmCIF format, chain C [auth A] mmCIF format, chain B [auth A]	B [auth A], C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain C [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.86 Å
R-Value Free: 0.232 (Depositor), 0.249 (DCC)
R-Value Work: 0.216 (Depositor)
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

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2022-01-12

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.