7FDP | pdb_00007fdp

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.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.231 (Depositor), 0.231 (DCC) 
• R-Value Work: 
  0.192 (Depositor), 0.192 (DCC) 
• R-Value Observed: 
  0.194 (Depositor) 

Starting Model: experimental

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

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

Macromolecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.231 (Depositor), 0.231 (DCC) 
• R-Value Work:  0.192 (Depositor), 0.192 (DCC) 
• R-Value Observed: 0.194 (Depositor) 

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

Entry History 

Deposition Data

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

Revision History  

• 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