9JWQ | pdb_00009jwq

De novo designed D-allose binding protein based on 1gud

• PDB DOI: https://doi.org/10.2210/pdb9JWQ/pdb

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


• Deposited: 2024-10-10 Released: 2025-10-15 
• Deposition Author(s): Wang, X., Liu, Y.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.255 (Depositor), 0.255 (DCC) 
• R-Value Work: 
  0.206 (Depositor), 0.206 (DCC) 
• R-Value Observed: 
  0.209 (Depositor) 

Starting Model: in silico

Literature

De novo designed D-allose binding protein based on 1gud

Wang, X., Liu, Y.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 29.79 kDa 
• Atom Count: 2,234 
• Modeled Residue Count: 286 
• Deposited Residue Count: 288 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MSD3-apo	A	288	synthetic construct	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.255 (Depositor), 0.255 (DCC) 
• R-Value Work:  0.206 (Depositor), 0.206 (DCC) 
• R-Value Observed: 0.209 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 34.158	α = 90
b = 56.263	β = 95.119
c = 64.77	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-10-15 
Deposition Author(s): Wang, X., Liu, Y.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2025-10-15
  Type: Initial release