7M5F | pdb_00007m5f

Contact-dependent inhibition system from Serratia marcescens BWH57

• PDB DOI: https://doi.org/10.2210/pdb7M5F/pdb

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


• Deposited: 2021-03-23 Released: 2021-05-12 
• Deposition Author(s): Michalska, K., Nutt, W., Stols, L., Jedrzejczak, R., Hayes, C.S., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.59 Å
• R-Value Free: 
  0.167 (Depositor), 0.169 (DCC) 
• R-Value Work: 
  0.140 (Depositor), 0.143 (DCC) 
• R-Value Observed: 
  0.142 (Depositor) 

Literature

Contact-dependent inhibition system from Serratia marcescens

Michalska, K., Nutt, W., Stols, L., Jedrzejczak, R., Hayes, C.S., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

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)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 27.25 kDa 
• Atom Count: 2,135 
• Modeled Residue Count: 217 
• Deposited Residue Count: 241 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CdiI	A	98	Serratia marcescens	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Toxin CdiA	B [auth C]	143	Serratia marcescens	Mutation(s): 0  Gene Names: SK68_03206

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MLI	C [auth A], D [auth C], E [auth C]	MALONATE ION C3 H2 O4 OFOBLEOULBTSOW-UHFFFAOYSA-L

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.59 Å
• R-Value Free:  0.167 (Depositor), 0.169 (DCC) 
• R-Value Work:  0.140 (Depositor), 0.143 (DCC) 
• R-Value Observed: 0.142 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m37m5f

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.691	α = 90
b = 97.241	β = 90
c = 44.495	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2021-05-12 
Deposition Author(s): Michalska, K., Nutt, W., Stols, L., Jedrzejczak, R., Hayes, C.S., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	HHSN272201700060C

Revision History  

• Version 1.0: 2021-05-12
  Type: Initial release
  
• Version 1.1: 2021-08-18
  Changes: Database references, Structure summary
• Version 1.2: 2024-10-23
  Changes: Data collection, Structure summary