5OP1 | pdb_00005op1

Designed Ankyrin Repeat Protein (DARPin) A4 in complex with Lysozyme

• PDB DOI: https://doi.org/10.2210/pdb5OP1/pdb

• Classification: DE NOVO PROTEIN
• Organism(s): synthetic construct, Gallus gallus
• Expression System: Escherichia coli M15
• Mutation(s): No 


• Deposited: 2017-08-09 Released: 2018-08-29 
• Deposition Author(s): Fischer, G., Hogan, B.J., Houlihan, G., Edmond, S., Huovinen, T.T.K., Hollfelder, F., Hyvonen, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.28 Å
• R-Value Free: 
  0.249 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.207 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.210 (Depositor) 

Starting Model: experimental

Literature

Designed Ankyrin Repeat Protein (DARPin) A4 in complex with Lysozyme

Fischer, G., Hyvonen, 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 Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 32.27 kDa 
• Atom Count: 2,213 
• Modeled Residue Count: 282 
• Deposited Residue Count: 297 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DARPin A4	A	168	synthetic construct	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Lysozyme C	B	129	Gallus gallus	Mutation(s): 0  EC: 3.2.1.17
UniProt
Find proteins for P00698 (Gallus gallus) Explore P00698  Go to UniProtKB:  P00698

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CL	C [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.28 Å
• R-Value Free:  0.249 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.207 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.210 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.916	α = 90
b = 102.866	β = 90
c = 50.277	γ = 90

Software Package:

Software Name	Purpose
Aimless	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-08-29 
Deposition Author(s): Fischer, G., Hogan, B.J., Houlihan, G., Edmond, S., Huovinen, T.T.K., Hollfelder, F., Hyvonen, M.

Revision History  

• Version 1.0: 2018-08-29
  Type: Initial release
  
• Version 1.1: 2024-01-17
  Changes: Data collection, Database references, Refinement description
• Version 1.2: 2024-11-06
  Changes: Structure summary