6K9A | pdb_00006k9a

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

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free:
0.248 (Depositor), 0.248 (DCC)
R-Value Work:
0.209 (Depositor), 0.208 (DCC)
R-Value Observed:
0.211 (Depositor)

wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment

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

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.

Macromolecule Content

Total Structure Weight: 35.45 kDa
Atom Count: 2,333
Modeled Residue Count: 279
Deposited Residue Count: 306
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Primase	A	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
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
DGT (Subject of Investigation/LOI) Query on DGT 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]	2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₃ P₃ HAAZLUGHYHWQIW-KVQBGUIXSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
CA Query on CA 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]	CALCIUM ION Ca BHPQYMZQTOCNFJ-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: 2.30 Å
R-Value Free: 0.248 (Depositor), 0.248 (DCC)
R-Value Work: 0.209 (Depositor), 0.208 (DCC)
R-Value Observed: 0.211 (Depositor)

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

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2020-06-17

Deposition Author(s):

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

Revision History (Full details and data files)

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

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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.