9K4Q | pdb_00009k4q

Crystal structure of designed zinc-induced homodimer C2-Zn1-HEHE-2

• PDB DOI: https://doi.org/10.2210/pdb9K4Q/pdb

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


• Deposited: 2024-10-21 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: 2.00 Å
• R-Value Free: 
  0.248 (Depositor), 0.255 (DCC) 
• R-Value Work: 
  0.190 (Depositor) 
• R-Value Observed: 
  0.196 (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 - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly Evidence: light scattering, equilibrium centrifugation

Macromolecule Content 

• Total Structure Weight: 26.09 kDa 
• Atom Count: 1,560 
• Modeled Residue Count: 178 
• Deposited Residue Count: 224 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
C2-Zn1-HEHE-2	A, B [auth C]	112	Escherichia coli	Mutation(s): 0

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.248 (Depositor), 0.255 (DCC) 
• R-Value Work:  0.190 (Depositor) 
• R-Value Observed: 0.196 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 30.643	α = 90
b = 93.272	β = 118.72
c = 31.779	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