6LEE | pdb_00006lee

Crystal structure of Cypovirus Polyhedra mutant with deletion of Ala67-Ala104

• PDB DOI: https://doi.org/10.2210/pdb6LEE/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Bombyx mori cypovirus 1
• Expression System: Spodoptera frugiperda
• Mutation(s): Yes 


• Deposited: 2019-11-25 Released: 2020-12-09 
• Deposition Author(s): Abe, S., Kasamatsu, M., Hirata, K., Yamashita, K., Ueno, T.
• Funding Organization(s): Japan Society for the Promotion of Science

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 
  0.250 (Depositor), 0.224 (DCC) 
• R-Value Work: 
  0.187 (Depositor) 
• R-Value Observed: 
  0.193 (Depositor) 

Starting Model: experimental

Literature

In-Cell Engineering of Protein Crystals with Nanoporous Structures for Promoting Cascade Reactions

Nguyen, T.K., Abe, S., Kasamatsu, M., Maity, B., Yamashita, K., Hirata, K., Kojima, M., Ueno, T.

(2021) ACS Appl Nano Mater 4: 1672-1681

• DOI: https://doi.org/10.1021/acsanm.0c03129

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 23.93 kDa 
• Atom Count: 1,661 
• Modeled Residue Count: 199 
• Deposited Residue Count: 210 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Polyhedrin	A	210	Bombyx mori cypovirus 1	Mutation(s): 1
UniProt
Find proteins for P11041 (Bombyx mori cytoplasmic polyhedrosis virus) Explore P11041  Go to UniProtKB:  P11041

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free:  0.250 (Depositor), 0.224 (DCC) 
• R-Value Work:  0.187 (Depositor) 
• R-Value Observed: 0.193 (Depositor) 

Space Group: I 2 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 103.84	α = 90
b = 103.84	β = 90
c = 103.84	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XSCALE	data scaling
PHENIX	phasing
XDS	data processing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2020-12-09 
Deposition Author(s): Abe, S., Kasamatsu, M., Hirata, K., Yamashita, K., Ueno, T.

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Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science	Japan	JP17H05872

Revision History  

• Version 1.0: 2020-12-09
  Type: Initial release
  
• Version 1.1: 2021-04-07
  Changes: Database references
• Version 1.2: 2021-04-14
  Changes: Database references
• Version 1.3: 2023-11-22
  Changes: Data collection, Database references, Refinement description
• Version 1.4: 2024-10-16
  Changes: Structure summary