9KGZ | pdb_00009kgz

Crystal structure of a de novo designed monomeric mainly-beta protein B10 (monoclinic)

• PDB DOI: https://doi.org/10.2210/pdb9KGZ/pdb

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


• Deposited: 2024-11-09 Released: 2025-07-02 
• Deposition Author(s): Zhang, Y., Liu, Y., Ma, Z., Li, M., Xu, C., Gong, H.
• Funding Organization(s): Ministry of Science and Technology (MoST, China), National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.200 (Depositor), 0.200 (DCC) 
• R-Value Work: 
  0.175 (Depositor), 0.175 (DCC) 
• R-Value Observed: 
  0.176 (Depositor) 

Starting Model: in silico

Literature

Crystal structure of a de novo designed monomeric mainly-beta protein B10 (monoclinic)

Zhang, Y., Liu, Y., Xu, C., Gong, H.

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: 14.26 kDa 
• Atom Count: 1,164 
• Modeled Residue Count: 125 
• Deposited Residue Count: 125 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
De novo designed monomeric mainly-beta protein B10	A	125	synthetic construct	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.200 (Depositor), 0.200 (DCC) 
• R-Value Work:  0.175 (Depositor), 0.175 (DCC) 
• R-Value Observed: 0.176 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.886	α = 90
b = 47.68	β = 97.96
c = 38.93	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-07-02 
Deposition Author(s): Zhang, Y., Liu, Y., Ma, Z., Li, M., Xu, C., Gong, H.

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Funding Organization	Location	Grant Number
Ministry of Science and Technology (MoST, China)	China	2023YFF1204400
National Natural Science Foundation of China (NSFC)	China	32171243

Revision History  

• Version 1.0: 2025-07-02
  Type: Initial release