7XGC | pdb_00007xgc

Crystal structure of influenza polymerase acidic subunit N-terminal domain crystallized by ammonium sulfate with glycan

PDB DOI: https://doi.org/10.2210/pdb7XGC/pdb

Classification: VIRAL PROTEIN
Organism(s): Influenza A virus (A/Puerto Rico/8/1934(H1N1))
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2022-04-04 Released: 2022-04-20
Deposition Author(s): Guo, Y., Hoshino, T.
Funding Organization(s): Japan Society for the Promotion of Science (JSPS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free:
0.228 (Depositor), 0.230 (DCC)
R-Value Work:
0.205 (Depositor), 0.210 (DCC)
R-Value Observed:
0.206 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Influence of Glycan Agents on Protein Crystallization with Ammonium Sulfate

Guo, Y., Hoshino, T.

(2022) Cryst Growth Des

DOI: https://doi.org/10.1021/acs.cgd.2c00901

Macromolecule Content

Total Structure Weight: 22.51 kDa
Atom Count: 1,584
Modeled Residue Count: 181
Deposited Residue Count: 191
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Polymerase acidic protein	A	191	Influenza A virus (A/Puerto Rico/8/1934(H1N1))	Mutation(s): 0 Gene Names: PA EC: 3.1
UniProt
Find proteins for P03433 (Influenza A virus (strain A/Puerto Rico/8/1934 H1N1)) Explore P03433 Go to UniProtKB: P03433
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P03433
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 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]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
MN Query on MN Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A]	C [auth A], D [auth A]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free: 0.228 (Depositor), 0.230 (DCC)
R-Value Work: 0.205 (Depositor), 0.210 (DCC)
R-Value Observed: 0.206 (Depositor)

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.177	α = 90
b = 66.177	β = 90
c = 125.727	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PDB_EXTRACT	data extraction
MOLREP	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2022-04-20

Deposition Author(s):

Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	21K07050

Revision History (Full details and data files)

Version 1.0: 2022-04-20
Type: Initial release
Version 1.1: 2022-11-02
Changes: Database references
Version 1.2: 2023-11-29
Changes: Data collection, Refinement description

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.