2BKG

Crystal structure of E3_19 a designed ankyrin repeat protein

• PDB DOI: https://doi.org/10.2210/pdb2BKG/pdb

• Classification: DE NOVO PROTEIN
• Organism(s): synthetic construct
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2005-02-16 Released: 2006-06-21 
• Deposition Author(s): Binz, H.K., Kohl, A., Pluckthun, A., Grutter, M.G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.227 
• R-Value Work: 0.176 
• R-Value Observed: 0.178 

Starting Model: experimental

Literature

Crystal Structure of a Consensus-Designed Ankyrin Repeat Protein: Implications for Stability

Binz, H.K., Kohl, A., Pluckthun, A., Grutter, M.G.

(2006) Proteins 65: 280

• PubMed: 16493627 
• DOI: https://doi.org/10.1002/prot.20930
• Primary Citation of Related Structures:  
  2BKG


• PubMed Abstract: 
  

  Consensus-designed ankyrin repeat (AR) proteins are thermodynamically very stable. The structural analysis of the designed AR protein E3_5 revealed that this stability is due to a regular fold with highly conserved structural motifs and H-bonding networks. However, the designed AR protein E3_19 exhibits a significantly lower stability than E3_5 (9.6 vs. 14.8 kcal/mol), despite 88% sequence identity. To investigate the structural correlations of this stability difference between E3_5 and E3_19, we determined the crystal structure of E3_19 at 1.9 A resolution. E3_19 as well has a regular AR domain fold with the characteristic H-bonding patterns. All structural features of the E3_5 and E3_19 molecules appear to be virtually identical (RMSD(Calpha) approximately 0.7 A). However, clear differences are observed in the surface charge distribution of the two AR proteins. E3_19 features clusters of charged residues and more exposed hydrophobic residues than E3_5. The atomic coordinates of E3_19 have been deposited in the Protein Data Bank. PDB ID: 2BKG.

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Organizational Affiliation: 

Biochemisches Institut, Universität Zürich, Zürich, Switzerland.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PQS (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content

• Total Structure Weight: 35.61 kDa 
• Atom Count: 2,660 
• Modelled Residue Count: 310 
• Deposited Residue Count: 332 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SYNTHETIC CONSTRUCT ANKYRIN REPEAT PROTEIN E3_19	A, B	166	synthetic construct	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.227 
• R-Value Work: 0.176 
• R-Value Observed: 0.178 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.579	α = 90
b = 72.67	β = 90
c = 83.325	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-06-21 
Deposition Author(s): Binz, H.K., Kohl, A., Pluckthun, A., Grutter, M.G.

Revision History  

• Version 1.0: 2006-06-21
  Type: Initial release
  
• Version 1.1: 2015-10-21
  Changes: Derived calculations, Non-polymer description, Other, Source and taxonomy, Structure summary, Version format compliance
• Version 1.2: 2022-10-19
  Changes: Database references, Other, Source and taxonomy
• Version 1.3: 2024-01-31
  Changes: Data collection, Refinement description