5YHA | pdb_00005yha

Crystal structure of Pd(allyl)/Wild Type Polyhedra

• PDB DOI: https://doi.org/10.2210/pdb5YHA/pdb

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


• Deposited: 2017-09-27 Released: 2017-11-29 
• Deposition Author(s): Abe, S., Atsumi, K., Yamashita, K., Hirata, K., Mori, H., Ueno, T.
• Funding Organization(s): Japan Society for the Promotion of Science

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.58 Å
• R-Value Free: 
  0.197 (Depositor), 0.204 (DCC) 
• R-Value Work: 
  0.150 (Depositor), 0.162 (DCC) 
• R-Value Observed: 
  0.154 (Depositor) 

Starting Model: experimental

Literature

Structure of in cell protein crystals containing organometallic complexes.

Abe, S., Atsumi, K., Yamashita, K., Hirata, K., Mori, H., Ueno, T.

(2018) Phys Chem Chem Phys 20: 2986-2989

• PubMed: 29138769 
• DOI: https://doi.org/10.1039/c7cp06651a
• Primary Citation Related Structures: 
  5YHA, 5YHB


• PubMed Abstract: 
  

  The molecular structures of in cell protein crystals containing organometallic Pd(allyl) complexes were determined by performing microfocus X-ray diffraction experiments. The coordination sites in a polyhedrin mutant with deletion of selected amino acid residues located at the interface of the polyhedrin trimer are dramatically altered compared to those of the wild-type composite.

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Organizational Affiliation: 
• School of Life Science and Technology, Tokyo Institute of Technology, Nagatsuta-cho, Midori-ku, Yokohama 226-8501, Japan. [e-mail] [e-mail].

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: 29.46 kDa 
• Atom Count: 2,146 
• Modeled Residue Count: 248 
• Deposited Residue Count: 248 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Polyhedrin	A	248	Bombyx mori cypovirus 1	Mutation(s): 1
UniProt
Find proteins for P11041 (Bombyx mori cytoplasmic polyhedrosis virus) Explore P11041  Go to UniProtKB:  P11041

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PLL	C [auth A], D [auth A], E [auth A]	Palladium(II) allyl complex C3 H5 Pd WTWGCTVOVPTEEU-UHFFFAOYSA-N
PD	F [auth A], G [auth A], H [auth A], I [auth A], J [auth A]	PALLADIUM ION Pd MUJIDPITZJWBSW-UHFFFAOYSA-N
EDO	K [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL	B [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.58 Å
• R-Value Free:  0.197 (Depositor), 0.204 (DCC) 
• R-Value Work:  0.150 (Depositor), 0.162 (DCC) 
• R-Value Observed: 0.154 (Depositor) 

Space Group: I 2 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 103.19	α = 90
b = 103.19	β = 90
c = 103.19	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2017-11-29 
Deposition Author(s): Abe, S., Atsumi, K., Yamashita, K., Hirata, K., Mori, H., Ueno, T.

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Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science	Japan	JP16H00827

Revision History  

• Version 1.0: 2017-11-29
  Type: Initial release
  
• Version 1.1: 2018-02-14
  Changes: Database references
• Version 1.2: 2023-11-22
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.3: 2024-10-09
  Changes: Structure summary