9LQK | pdb_00009lqk

Crystal structure of synthetic ubiquitin variant R10 designed by ProteinMPNN

• PDB DOI: https://doi.org/10.2210/pdb9LQK/pdb

• Classification: DE NOVO PROTEIN
• Organism(s): synthetic construct
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2025-01-28 Released: 2025-02-12 
• Deposition Author(s): Lu, W.-L., Ko, T.-P., Wu, K.-P.
• Funding Organization(s): Academia Sinica (Taiwan), Ministry of Science and Technology (MoST, Taiwan)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free: 
  0.229 (Depositor), 0.229 (DCC) 
• R-Value Work: 
  0.191 (Depositor), 0.192 (DCC) 
• R-Value Observed: 
  0.193 (Depositor) 

Starting Model: in silico

Literature

Crystal structure of synthetic ubiquitin variant R10 designed by ProteinMPNN

Wu, K.-P.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: light scattering

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 23.46 kDa 
• Atom Count: 1,456 
• Modeled Residue Count: 158 
• Deposited Residue Count: 206 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ubiquitin variant R10	A, B	103	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	C [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free:  0.229 (Depositor), 0.229 (DCC) 
• R-Value Work:  0.191 (Depositor), 0.192 (DCC) 
• R-Value Observed: 0.193 (Depositor) 

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.556	α = 90
b = 62.548	β = 90
c = 89.757	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Coot	model building
Blu-Ice	data collection
HKL-2000	data scaling
PHASER	phasing
HKL-2000	data reduction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-02-12 
Deposition Author(s): Lu, W.-L., Ko, T.-P., Wu, K.-P.

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Funding Organization	Location	Grant Number
Academia Sinica (Taiwan)	Taiwan	AS-GCS-113-L05
Academia Sinica (Taiwan)	Taiwan	AS-CDA-110-L03
Ministry of Science and Technology (MoST, Taiwan)	Taiwan	NSTC-113-2113-M-001-030

Revision History  

• Version 1.0: 2025-02-12
  Type: Initial release