3GKL | pdb_00003gkl

Following evolutionary paths to high affinity and selectivity protein-protein interactions using Colicin7 and Immunity proteins

• PDB DOI: https://doi.org/10.2210/pdb3GKL/pdb

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


• Deposited: 2009-03-11 Released: 2009-09-08 
• Deposition Author(s): Dym, O., Tawfik, D.S., Israel Structural Proteomics Center (ISPC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.277 (Depositor), 0.310 (DCC) 
• R-Value Work: 
  0.240 (Depositor), 0.270 (DCC) 
• R-Value Observed: 
  0.241 (Depositor) 

Starting Model: experimental

Literature

Following evolutionary paths to high affinity and selectivity protein-protein interactions

Bernath, K., Dym, O., Albeck, S., Magdassi, S., Keeble, A., Kleanthous, C., Tawfik, D.S.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 51.6 kDa 
• Atom Count: 3,223 
• Modeled Residue Count: 404 
• Deposited Residue Count: 454 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Colicin-E9 immunity protein	A, B	141	Escherichia coli	Mutation(s): 9  Gene Names: colE7, cea EC: 3.1
UniProt
Find proteins for Q47112 (Escherichia coli) Explore Q47112  Go to UniProtKB:  Q47112

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Colicin-E7	C, D	86	Escherichia coli	Mutation(s): 9  Gene Names: imm, ceiE9
UniProt
Find proteins for P13479 (Escherichia coli) Explore P13479  Go to UniProtKB:  P13479

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	E [auth A], F [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.277 (Depositor), 0.310 (DCC) 
• R-Value Work:  0.240 (Depositor), 0.270 (DCC) 
• R-Value Observed: 0.241 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.161	α = 90
b = 67.371	β = 90
c = 123.231	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-09-08 
Deposition Author(s): Dym, O., Tawfik, D.S., Israel Structural Proteomics Center (ISPC)

Revision History  

• Version 1.0: 2009-09-08
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2021-10-20
  Changes: Database references, Derived calculations
• Version 1.3: 2023-09-06
  Changes: Data collection, Refinement description