Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Icosahedral - I  (3D View)
Global Stoichiometry: Homo 180-mer - A180 

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

Macromolecule Content

• Total Structure Weight: 1455.55 kDa 
• Atom Count: 101490 
• Residue Count: 12990 
• Unique protein chains: 1

6YFN

Virus-like particle of bacteriophage ESE058

• DOI: 10.2210/pdb6YFN/pdb

• Classification: VIRUS LIKE PARTICLE
• Organism(s): Leviviridae sp.
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2020-03-26 Released: 2020-09-02 
• Deposition Author(s): Rumnieks, J., Kalnins, G., Sisovs, M., Lieknina, I., Tars, K.
• Funding Organization(s): European Regional Development Fund

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.19 Å
• R-Value Free: 0.234 
• R-Value Work: 0.231 
• R-Value Observed: 0.231 

Literature

Expansion of the structural diversity of single-stranded RNA bacteriophages

Rumnieks, J., Kalnins, G., Sisovs, M., Lieknina, i., Tars, K.

To be published.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
coat protein	AA, AB, AC, AD, AE, AF, AG, AH, AI, AJ, AK, AL, AM, AN, AO, AP, AQ, AR, AS, AT, AU, AV, AW, AX, AY, AZ, BA, BB, BC, BD, BE, BF, BG, BH, BI, BJ, BK, BL, BM, BN, BO, BP, BQ, BR, BS, BT, BU, BV, BW, BX, BY, BZ, CA, CB, CC, CD, CE, CF, CG, CH, CI, CJ, CK, CL, CM, CN, CO, CP, CQ, CR, CS, CT, CU, CV, CW, CX, CY, CZ, DA, DB, DC, DD, DE, DF, DG, DH, DI, DJ, DK, DL	146	Leviviridae sp.	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	AC, AF, AI, AL, AO, AR, AU, AX, BA, BD, BG, BJ, BM, BP, BS, BV, BY, CE	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.19 Å
• R-Value Free: 0.234 
• R-Value Work: 0.231 
• R-Value Observed: 0.231 
• Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 500.893	α = 90
b = 500.893	β = 90
c = 287.055	γ = 120

Software Package:

Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
FFT	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2020-03-26 
• Released Date: 2020-09-02 
Deposition Author(s): Rumnieks, J., Kalnins, G., Sisovs, M., Lieknina, I., Tars, K.

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Funding Organization	Location	Grant Number
European Regional Development Fund	Latvia	1.1.1.1/16/A/104

Revision History 

• Version 1.0: 2020-09-02
  Type: Initial release