7FDP

Crystal structure of PirB insecticidal protein from Photorhabdus akhurstii

PDB DOI: https://doi.org/10.2210/pdb7FDP/pdb

Classification: TOXIN
Organism(s): Photorhabdus akhurstii
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2021-07-17 Released: 2022-07-20
Deposition Author(s): Prashar, A., Kinkar, O., Kumar, A., Hire, R.S., Makde, R.D.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.231
R-Value Work: 0.192
R-Value Observed: 0.194

wwPDB Validation 3D Report Full Report

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

Literature

Crystal structures of PirA and PirB toxins from Photorhabdus akhurstii subsp. akhurstii K-1

Prashar, A., Kinkar, O.U., Kumar, A., Hadapad, A.B., Makde, R.D., Hire, R.S.

(2023) Insect Biochem Mol Biol 162: 104014

DOI: https://doi.org/10.1016/j.ibmb.2023.104014

Macromolecule Content

Total Structure Weight: 92.69 kDa
Atom Count: 6,896
Modelled Residue Count: 805
Deposited Residue Count: 838
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Insecticidal protein	A, B	419	Photorhabdus akhurstii	Mutation(s): 0 Gene Names: pirB
UniProt
Find proteins for G5DBH4 (Photorhabdus akhurstii) Explore G5DBH4 Go to UniProtKB: G5DBH4
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	G5DBH4
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.231
R-Value Work: 0.192
R-Value Observed: 0.194
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.802	α = 90
b = 89.274	β = 90
c = 124.657	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
Aimless	data scaling
PHASER	phasing
PHENIX	model building
PHENIX	refinement
Coot	model building

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2022-07-20

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2022-07-20
Type: Initial release
Version 1.1: 2023-10-25
Changes: Data collection, Database references
Version 1.2: 2023-11-29
Changes: 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 R01GM133198.