5OP3 | pdb_00005op3

Designed Ankyrin Repeat Protein (DARPin) NDNH-1 selected by directed evolution against Lysozyme

• PDB DOI: https://doi.org/10.2210/pdb5OP3/pdb

• Classification: DE NOVO PROTEIN
• Organism(s): synthetic construct
• Expression System: Escherichia coli
• 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: 1.36 Å
• R-Value Free: 
  0.161 (Depositor), 0.163 (DCC) 
• R-Value Work: 
  0.133 (Depositor), 0.134 (DCC) 
• R-Value Observed: 
  0.134 (Depositor) 

Starting Model: experimental

Literature

Designed Ankyrin Repeat Protein (DARPin) NDNH-1 selected by directed evolution against Lysozyme

Fischer, G., Hyvonen, M.

To be published.

Biological Assembly 1  

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

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 18.21 kDa 
• Atom Count: 1,477 
• Modeled Residue Count: 157 
• Deposited Residue Count: 168 
• Unique protein chains: 1

Macromolecules

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

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ACT	B [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
CA	C [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL	D [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.36 Å
• R-Value Free:  0.161 (Depositor), 0.163 (DCC) 
• R-Value Work:  0.133 (Depositor), 0.134 (DCC) 
• R-Value Observed: 0.134 (Depositor) 

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 120.746	α = 90
b = 120.746	β = 90
c = 24.653	γ = 120

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, Derived calculations, Refinement description