5OOU | pdb_00005oou

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

PDB DOI: https://doi.org/10.2210/pdb5OOU/pdb

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

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

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.206 (Depositor), 0.210 (DCC)
R-Value Work:
0.185 (Depositor), 0.190 (DCC)
R-Value Observed:
0.186 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

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

Fischer, G., Hyvonen, M.

To be published.

Macromolecule Content

Total Structure Weight: 18.11 kDa
Atom Count: 1,339
Modeled Residue Count: 165
Deposited Residue Count: 168
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DARPin YTRL-1	A	168	synthetic construct	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.206 (Depositor), 0.210 (DCC)
R-Value Work: 0.185 (Depositor), 0.190 (DCC)
R-Value Observed: 0.186 (Depositor)

Space Group: P 6₄ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 103.5	α = 90
b = 103.5	β = 90
c = 96.13	γ = 120

Software Package:

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

Structure Validation

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Entry History

Deposition Data

Released Date: 2018-08-29

Deposition Author(s):

Huovinen, T.T.K.

Revision History (Full details and data files)

Version 1.0: 2018-08-29
Type: Initial release
Version 1.1: 2024-01-17
Changes: Data collection, Database references, Refinement description

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.