5OOS | pdb_00005oos

Designed Ankyrin Repeat Protein (DARPin) YTRL-2 selected by directed evolution against Lysozyme

PDB DOI: https://doi.org/10.2210/pdb5OOS/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): Hogan, B.J., Fischer, G., Houlihan, G., Edmond, S., Huovinen, T.T.K., Hollfelder, F., Hyvonen, M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.26 Å
R-Value Free:
0.226 (Depositor), 0.231 (DCC)
R-Value Work:
0.196 (Depositor), 0.200 (DCC)
R-Value Observed:
0.198 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 5OOS

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

Literature

Designed Ankyrin Repeat Protein (DARPin) YTRL-2 selected by directed evolution against Lysozyme

Fischer, G.

To be published.

Macromolecule Content

Total Structure Weight: 18.61 kDa
Atom Count: 1,317
Modeled Residue Count: 161
Deposited Residue Count: 168
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DARPin YTRL-2	A	168	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
2PE Query on 2PE Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	NONAETHYLENE GLYCOL C₁₈ H₃₈ O₁₀ YZUUTMGDONTGTN-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.26 Å
R-Value Free: 0.226 (Depositor), 0.231 (DCC)
R-Value Work: 0.196 (Depositor), 0.200 (DCC)
R-Value Observed: 0.198 (Depositor)

Space Group: P 6₄ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 102.487	α = 90
b = 102.487	β = 90
c = 96.714	γ = 120

Software Package:

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

Structure Validation

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View more in-depth experimental data

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: 2024-05-08
Changes: Data collection, Database references

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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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.