9K7X | pdb_00009k7x

Crystal structure of designed calcium-induced homotrimer C3-Ca1-DN*3-20

• PDB DOI: https://doi.org/10.2210/pdb9K7X/pdb

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


• Deposited: 2024-10-24 Released: 2025-10-29 
• Deposition Author(s): Qu, Y.N., Cao, L.X.
• Funding Organization(s): Ministry of Science and Technology (MoST, China)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.227 (Depositor), 0.227 (DCC) 
• R-Value Work: 
  0.172 (Depositor), 0.172 (DCC) 
• R-Value Observed: 
  0.176 (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 - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

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

Biological Assembly Evidence: equilibrium centrifugation, light scattering

Biological Assembly 2  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 75.07 kDa 
• Atom Count: 4,473 
• Modeled Residue Count: 531 
• Deposited Residue Count: 672 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
C3-Ca1-DN*3-20	A, B, C, D, E, F	112	Escherichia coli	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TRS	J [auth D]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C4 H12 N O3 LENZDBCJOHFCAS-UHFFFAOYSA-O
CA (Subject of Investigation/LOI)	G [auth A], H [auth A], I [auth C]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.227 (Depositor), 0.227 (DCC) 
• R-Value Work:  0.172 (Depositor), 0.172 (DCC) 
• R-Value Observed: 0.176 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 34.614	α = 90
b = 77.562	β = 92.46
c = 82.814	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: 2025-10-29 
Deposition Author(s): Qu, Y.N., Cao, L.X.

---

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

Revision History  

• Version 1.0: 2025-10-29
  Type: Initial release