2GYK

Crystal structure of the complex of the Colicin E9 DNase domain with a mutant immunity protein, IMME9 (D51A)

• PDB DOI: https://doi.org/10.2210/pdb2GYK/pdb

• Classification: antibiotic/antibiotic inhibitor
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli BL21(DE3), Escherichia coli
• Mutation(s): Yes 


• Deposited: 2006-05-09 Released: 2007-05-15 
• Deposition Author(s): Santi, P.S., Kolade, O.O., Kuhlmann, U.C., Hemmings, A.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.232 
• R-Value Work: 0.185 
• R-Value Observed: 0.187 

Literature

Crystal structures of the complexes of the Colicin E9 DNase domain with mutant immunity proteins

Kuhlmann, U.C., Santi, P.S., Kolade, O.O., Moore, G.R., James, R., Kleanthous, C., Hemmings, A.M.

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 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 49.66 kDa 
• Atom Count: 4,109 
• Modelled Residue Count: 428 
• Deposited Residue Count: 440 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Colicin-E9 immunity protein	A, C [auth E]	86	Escherichia coli K-12	Mutation(s): 1  Gene Names: IMM9_ECOLI
UniProt
Find proteins for P13479 (Escherichia coli) Explore P13479  Go to UniProtKB:  P13479

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Colicin-E9	B, D [auth F]	134	Escherichia coli K-12	Mutation(s): 0  Gene Names: col, cei EC: 3.1.21.1
UniProt
Find proteins for P09883 (Escherichia coli) Explore P09883  Go to UniProtKB:  P09883

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	F [auth B], H [auth F]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
ZN	E [auth B], G [auth F]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.232 
• R-Value Work: 0.185 
• R-Value Observed: 0.187 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.903	α = 90
b = 88.248	β = 91.92
c = 52.235	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-05-15 
Deposition Author(s): Santi, P.S., Kolade, O.O., Kuhlmann, U.C., Hemmings, A.M.

Revision History  

• Version 1.0: 2007-05-15
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-18
  Changes: Data collection, Refinement description
• Version 1.4: 2021-10-20
  Changes: Database references, Derived calculations
• Version 1.5: 2023-08-30
  Changes: Data collection, Refinement description