8ZAW | pdb_00008zaw

Crystal structure of PNPase in Anabaena

PDB DOI: https://doi.org/10.2210/pdb8ZAW/pdb

Classification: RNA BINDING PROTEIN
Organism(s): Anabaena
Expression System: Escherichia
Mutation(s): No

Deposited: 2024-04-25 Released: 2025-04-30
Deposition Author(s): Peng, Y.J.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free:
0.286 (Depositor), 0.290 (DCC)
R-Value Work:
0.231 (Depositor), 0.232 (DCC)
R-Value Observed:
0.233 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 8ZAW

This is version 1.0 of the entry. See complete history.

Literature

Structure of PNPase in Anabaena

Peng, Y.J.

To be published.

Macromolecule Content

Total Structure Weight: 79.36 kDa
Atom Count: 3,780
Modeled Residue Count: 492
Deposited Residue Count: 731
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Polyribonucleotide nucleotidyltransferase	A	731	Anabaena	Mutation(s): 0 Gene Names: pnp, all4396 EC: 2.7.7.8
UniProt
Find proteins for Q8YP11 (Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576)) Explore Q8YP11 Go to UniProtKB: Q8YP11
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8YP11
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MG (Subject of Investigation/LOI) Query on MG Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free: 0.286 (Depositor), 0.290 (DCC)
R-Value Work: 0.231 (Depositor), 0.232 (DCC)
R-Value Observed: 0.233 (Depositor)

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 89.119	α = 90
b = 89.119	β = 90
c = 194.45	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2025-04-30

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2025-04-30
Type: Initial release

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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.