1BXI

CRYSTAL STRUCTURE OF THE ESCHERICHIA COLI COLICIN E9 DNASE DOMAIN WITH ITS COGNATE IMMUNITY PROTEIN IM9

• PDB DOI: https://doi.org/10.2210/pdb1BXI/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 1998-10-04 Released: 1999-10-04 
• Deposition Author(s): Kuhlmann, U.C., Kleanthous, C., James, R., Moore, G.R., Hemmings, A.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 
  0.315 (Depositor), 0.300 (DCC) 
• R-Value Work: 
  0.218 (Depositor), 0.210 (DCC) 

Literature

Crystal Structure of the E.Coli Colicin E9 DNase Domain With its Cognate Immunity Protein Im9

Kuhlmann, U.C.

(1998) Thesis 

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: 24.89 kDa 
• Atom Count: 1,794 
• Modelled Residue Count: 214 
• Deposited Residue Count: 220 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN (COLICIN E9 IMMUNITY PROTEIN)	A	86	Escherichia coli	Mutation(s): 1  Gene Names: E9IMM
UniProt
Find proteins for P13479 (Escherichia coli) Explore P13479  Go to UniProtKB:  P13479

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN (COLICIN E9)	B	134	Escherichia coli	Mutation(s): 2  Gene Names: COLE9 EC: 3.1
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	D [auth B]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
NI	C [auth B]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free:  0.315 (Depositor), 0.300 (DCC) 
• R-Value Work:  0.218 (Depositor), 0.210 (DCC) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.85	α = 90
b = 51.96	β = 90
c = 87.59	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 1999-10-04 
Deposition Author(s): Kuhlmann, U.C., Kleanthous, C., James, R., Moore, G.R., Hemmings, A.M.

Revision History  

• Version 1.0: 1999-10-04
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2018-03-14
  Changes: Data collection, Database references
• Version 1.4: 2021-11-03
  Changes: Database references, Derived calculations
• Version 1.5: 2023-12-27
  Changes: Data collection
• Version 1.6: 2024-11-13
  Changes: Structure summary