9LNI | pdb_00009lni

Crystal structure of the de novo designed protein ZZ1

• PDB DOI: https://doi.org/10.2210/pdb9LNI/pdb

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


• Deposited: 2025-01-21 Released: 2025-06-04 
• Deposition Author(s): Zhao, Z., Hattori, M.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.61 Å
• R-Value Free: 
  0.243 (Depositor), 0.242 (DCC) 
• R-Value Work: 
  0.208 (Depositor), 0.208 (DCC) 
• R-Value Observed: 
  0.210 (Depositor) 

Starting Model: in silico

Literature

Bioinformatics classification of the MgtE Mg2+ channel and de novo protein design for the stabilization of its novel subclass

Zhao, Z., Omae, K., Iwasaki, W., Zhang, Z., Pan, F., Lee, E., Ito, K., Hattori, M.

(2026) Acta Biochim Biophys Sin (Shanghai) 

• DOI: https://doi.org/10.3724/abbs.2025224

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 25.41 kDa 
• Atom Count: 1,909 
• Modeled Residue Count: 212 
• Deposited Residue Count: 212 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ZZ1	A	212	Escherichia coli	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	B [auth A], C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.61 Å
• R-Value Free:  0.243 (Depositor), 0.242 (DCC) 
• R-Value Work:  0.208 (Depositor), 0.208 (DCC) 
• R-Value Observed: 0.210 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 35.281	α = 90
b = 67.38	β = 108.52
c = 43.742	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-06-04 
Deposition Author(s): Zhao, Z., Hattori, M.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	--

Revision History  

• Version 1.0: 2025-06-04
  Type: Initial release
  
• Version 1.1: 2026-05-06
  Changes: Database references