2B5U | pdb_00002b5u

Crystal Structure Of Colicin E3 V206C Mutant In Complex With Its Immunity Protein

• PDB DOI: https://doi.org/10.2210/pdb2B5U/pdb

• Classification: RIBOSOME INHIBITOR, HYDROLASE
• Organism(s): Escherichia coli
• Expression System: Escherichia coli str. K-12 substr. W3110
• Mutation(s): Yes 


• Deposited: 2005-09-29 Released: 2006-11-07 
• Deposition Author(s): Nallini Vijayarangan, A., Nithianantham, S., Nan, W., Jakes, K., Shoham, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.295 (Depositor), 0.280 (DCC) 
• R-Value Work: 
  0.259 (Depositor), 0.240 (DCC) 
• R-Value Observed: 
  0.291 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure Of Colicin E3 In Complex With Its Immunity Protein

Nallini Vijayarangan, A., Nithianantham, S., Nan, W., Jakes, K., Shoham, 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: 136.04 kDa 
• Atom Count: 8,791 
• Modelled Residue Count: 1,108 
• Deposited Residue Count: 1,270 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Colicin E3	A, C	551	Escherichia coli	Mutation(s): 1  Gene Names: ceaC EC: 3.1 (PDB Primary Data), 4.6.1 (UniProt)
UniProt
Find proteins for P00646 (Escherichia coli) Explore P00646  Go to UniProtKB:  P00646

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Colicin E3 immunity protein	B, D	84	Escherichia coli	Mutation(s): 0  Gene Names: imm, ceiC, immB
UniProt
Find proteins for P02984 (Escherichia coli) Explore P02984  Go to UniProtKB:  P02984

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CIT	E [auth A], F [auth C]	CITRIC ACID C6 H8 O7 KRKNYBCHXYNGOX-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.295 (Depositor), 0.280 (DCC) 
• R-Value Work:  0.259 (Depositor), 0.240 (DCC) 
• R-Value Observed: 0.291 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.73	α = 90
b = 192.916	β = 112.98
c = 85.385	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
CNS	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-11-07 
Deposition Author(s): Nallini Vijayarangan, A., Nithianantham, S., Nan, W., Jakes, K., Shoham, M.

Revision History  

• Version 1.0: 2006-11-07
  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: 2017-10-11
  Changes: Refinement description
• Version 1.4: 2021-10-20
  Changes: Database references, Derived calculations
• Version 1.5: 2023-08-23
  Changes: Data collection, Refinement description