9LQM | pdb_00009lqm

Crystal structure of synthetic ubiquitin variant R4 designed by ProteinMPNN

• PDB DOI: https://doi.org/10.2210/pdb9LQM/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: 1.39 Å
• R-Value Free: 
  0.196 (Depositor), 0.195 (DCC) 
• R-Value Work: 
  0.164 (Depositor), 0.164 (DCC) 
• R-Value Observed: 
  0.165 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of synthetic ubiquitin variant R4 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: 23.91 kDa 
• Atom Count: 1,540 
• Modelled Residue Count: 161 
• Deposited Residue Count: 206 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ubiquitin variant R4	A, B	103	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth A], D [auth A], E [auth A], F [auth A], G [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.39 Å
• R-Value Free:  0.196 (Depositor), 0.195 (DCC) 
• R-Value Work:  0.164 (Depositor), 0.164 (DCC) 
• R-Value Observed: 0.165 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.845	α = 90
b = 50.845	β = 90
c = 102.666	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
Coot	model building
HKL-2000	data scaling
PHASER	phasing

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