2GZE

Crystal structure of the E9 DNase domain with a mutant immunity protein IM9 (Y55A)

• PDB DOI: https://doi.org/10.2210/pdb2GZE/pdb

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


• Deposited: 2006-05-11 Released: 2008-03-18 
• Deposition Author(s): Santi, P.S., Kolade, O.O., Kuhlmann, U.C., Kleanthous, C., Hemmings, A.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.242 
• R-Value Work: 0.184 
• R-Value Observed: 0.187 

Starting Model: experimental

Literature

Crystal Structure of the Complex of the Colicin E9 DNase Domain with a Mutant Immunity Protein, IM9 (Y55A)

Kuhlmann, U.C., Santi, P.S., Kolade, O.O., 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)

Macromolecule Content

• Total Structure Weight: 24.78 kDa 
• Atom Count: 1,993 
• Modelled Residue Count: 214 
• Deposited Residue Count: 220 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Colicin-E9 immunity protein	A	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	134	Escherichia coli K-12	Mutation(s): 0  Gene Names: col, cei EC: 3.1.21.1 (PDB Primary Data), 3.1 (UniProt)
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	D [auth B]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
ZN	C [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.242 
• R-Value Work: 0.184 
• R-Value Observed: 0.187 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.761	α = 90
b = 52.459	β = 90
c = 87.636	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: 2008-03-18 
Deposition Author(s): Santi, P.S., Kolade, O.O., Kuhlmann, U.C., Kleanthous, C., Hemmings, A.M.

Revision History  

• Version 1.0: 2008-03-18
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-10-18
  Changes: Data collection, Refinement description
• Version 1.3: 2021-10-20
  Changes: Database references, Derived calculations
• Version 1.4: 2023-08-30
  Changes: Data collection, Refinement description