9K6O | pdb_00009k6o

Crystal structure of designed zinc-induced homopentamer C5-Zn1-HEHE-1

• PDB DOI: https://doi.org/10.2210/pdb9K6O/pdb

• Classification: METAL BINDING PROTEIN
• Organism(s): Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-10-22 Released: 2025-10-22 
• Deposition Author(s): Qu, Y.N., Cao, L.X.
• Funding Organization(s): Ministry of Science and Technology (MoST, China)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free: 
  0.241 (Depositor), 0.242 (DCC) 
• R-Value Work: 
  0.188 (Depositor), 0.188 (DCC) 
• R-Value Observed: 
  0.192 (Depositor) 

Starting Model: in silico

Literature

De novo design of metal ion regulated protein assemblies

Qu, Y.N., Cao, L.X.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C5  (Explore in 3D)
Global Stoichiometry: Homo 5-mer - A5 

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

Biological Assembly Evidence: equilibrium centrifugation

Macromolecule Content 

• Total Structure Weight: 63.5 kDa 
• Atom Count: 3,823 
• Modeled Residue Count: 455 
• Deposited Residue Count: 560 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
C5-Zn1-HEHE-1	A, B, C, D, E	112	Escherichia coli	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN (Subject of Investigation/LOI)	F [auth A], G [auth A], H [auth C], I [auth C], J [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free:  0.241 (Depositor), 0.242 (DCC) 
• R-Value Work:  0.188 (Depositor), 0.188 (DCC) 
• R-Value Observed: 0.192 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 38.135	α = 90
b = 108.329	β = 95.64
c = 54.577	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
CrysalisPro	data reduction
CrysalisPro	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-10-22 
Deposition Author(s): Qu, Y.N., Cao, L.X.

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Funding Organization	Location	Grant Number
Ministry of Science and Technology (MoST, China)	China	--

Revision History  

• Version 1.0: 2025-10-22
  Type: Initial release