5FFP | pdb_00005ffp

Crystal structure of CdiI from Burkholderia dolosa AUO158

• PDB DOI: https://doi.org/10.2210/pdb5FFP/pdb

• Classification: ANTITOXIN
• Organism(s): Burkholderia dolosa AU0158
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2015-12-18 Released: 2016-01-20 
• Deposition Author(s): Michalska, K., Stols, L., Eschenfeldt, W., Goulding, C.W., Joachimiak, A., Midwest Center for Structural Genomics (MCSG), Structure-Function Analysis of Polymorphic CDI Toxin-Immunity Protein Complexes (UC4CDI)
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.205 (Depositor), 0.180 (DCC) 
• R-Value Work: 
  0.190 (Depositor), 0.166 (DCC) 
• R-Value Observed: 
  0.192 (Depositor) 

Literature

Crystal structure of CdiI from Burkholderia dolosa AUO158

Michalska, K., Stols, L., Eschenfeldt, W., Goulding, C.W., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 39 kDa 
• Atom Count: 2,440 
• Modeled Residue Count: 310 
• Deposited Residue Count: 344 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Immunity 23 family protein	A, B	172	Burkholderia dolosa AU0158	Mutation(s): 0  Gene Names: AK34_4389

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EPE	C [auth B]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C8 H18 N2 O4 S JKMHFZQWWAIEOD-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.205 (Depositor), 0.180 (DCC) 
• R-Value Work:  0.190 (Depositor), 0.166 (DCC) 
• R-Value Observed: 0.192 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M35FFP

Space Group: P 6₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 116.298	α = 90
b = 116.298	β = 90
c = 70.065	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2016-01-20 
Deposition Author(s): Michalska, K., Stols, L., Eschenfeldt, W., Goulding, C.W., Joachimiak, A., Midwest Center for Structural Genomics (MCSG), Structure-Function Analysis of Polymorphic CDI Toxin-Immunity Protein Complexes (UC4CDI)

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM094585
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM102318

Revision History  

• Version 1.0: 2016-01-20
  Type: Initial release
  
• Version 1.1: 2017-09-20
  Changes: Author supporting evidence, Derived calculations
• Version 1.2: 2019-12-25
  Changes: Author supporting evidence
• Version 1.3: 2024-11-06
  Changes: Data collection, Database references, Refinement description, Structure summary