5KIS | pdb_00005kis

YenB/RHS2 complex

• PDB DOI: https://doi.org/10.2210/pdb5KIS/pdb

• Classification: TOXIN
• Organism(s): Yersinia entomophaga
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2016-06-16 Released: 2017-08-09 
• Deposition Author(s): Busby, J.N., Hurst, M.R.H., Lott, J.S.
• Funding Organization(s): Marsden Fund

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.260 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.216 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.218 (Depositor) 

Starting Model: experimental

Literature

Structure of a new BC complex from Yersinia entomophaga

Busby, J.N., Hurst, M.R.H., Lott, J.S.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Macromolecule Content 

• Total Structure Weight: 274.3 kDa 
• Atom Count: 16,842 
• Modeled Residue Count: 2,121 
• Deposited Residue Count: 2,456 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
YenB	A	1,491	Yersinia entomophaga	Mutation(s): 0  Gene Names: yenB
UniProt
Find proteins for B6A880 (Yersinia entomophaga) Explore B6A880  Go to UniProtKB:  B6A880

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
RHS2	B	965	Yersinia entomophaga	Mutation(s): 0  Gene Names: RHS2
UniProt
Find proteins for A0A2D0TC51 (Yersinia entomophaga) Explore A0A2D0TC51  Go to UniProtKB:  A0A2D0TC51

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	C [auth A], H [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL	F [auth A], G [auth A], I [auth B], J [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	D [auth A], E [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.260 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.216 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.218 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 148.607	α = 90
b = 132.765	β = 103.85
c = 155.361	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2017-08-09 
Deposition Author(s): Busby, J.N., Hurst, M.R.H., Lott, J.S.

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Funding Organization	Location	Grant Number
Marsden Fund	New Zealand	UOA1406

Revision History  

• Version 1.0: 2017-08-09
  Type: Initial release
  
• Version 1.1: 2023-09-27
  Changes: Data collection, Database references, Derived calculations, Refinement description