9J9O | pdb_00009j9o

artificial dinuclear Zn-bound metalloprotein 1 (D1:2Zn)

• PDB DOI: https://doi.org/10.2210/pdb9J9O/pdb

• Classification: MEMBRANE PROTEIN
• Organism(s): Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): No 
• Membrane Protein: Yes  MemProtMD


• Deposited: 2024-08-23 Released: 2025-07-02 
• Deposition Author(s): Jeong, W.J., Song, W.J.
• Funding Organization(s): Other private

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.99 Å
• R-Value Free: 
  0.239 (Depositor), 0.241 (DCC) 
• R-Value Work: 
  0.192 (Depositor), 0.193 (DCC) 
• R-Value Observed: 
  0.195 (Depositor) 

Starting Model: experimental

Literature

Metal-Installer: A protein designer tool to create metal-binding sites

Jeong, W.J., Song, W.J.

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 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: 74.26 kDa 
• Atom Count: 5,172 
• Modeled Residue Count: 680 
• Deposited Residue Count: 680 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Outer membrane porin F	A, B	340	Escherichia coli	Mutation(s): 0  Gene Names: ompF, cmlB, coa, cry, tolF, b0929, JW0912 Membrane Entity: Yes
UniProt
Find proteins for P02931 (Escherichia coli (strain K12)) Explore P02931  Go to UniProtKB:  P02931

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.99 Å
• R-Value Free:  0.239 (Depositor), 0.241 (DCC) 
• R-Value Work:  0.192 (Depositor), 0.193 (DCC) 
• R-Value Observed: 0.195 (Depositor) 

Space Group: P 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 137.8	α = 90
b = 137.8	β = 90
c = 49.545	γ = 120

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-07-02 
Deposition Author(s): Jeong, W.J., Song, W.J.

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Funding Organization	Location	Grant Number
Other private	Korea, Republic Of	2019R1C1C1003863

Revision History  

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