9J9L | pdb_00009j9l

artificial mononuclear Zn-bound metalloprotein 1 (M1:Zn)

• PDB DOI: https://doi.org/10.2210/pdb9J9L/pdb

• Classification: MEMBRANE PROTEIN
• Organism(s): Escherichia coli (strain K12)
• Mutation(s): No 


• Deposited: 2024-08-22 Released: 2025-07-02 
• Deposition Author(s): Jeong, W.J., Song, W.J.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 
  0.278 (Depositor), 0.278 (DCC) 
• R-Value Work: 
  0.195 (Depositor), 0.195 (DCC) 
• R-Value Observed: 
  0.199 (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)

Macromolecule Content 

• Total Structure Weight: 37.26 kDa 
• Atom Count: 2,676 
• Modeled Residue Count: 339 
• Deposited Residue Count: 340 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Outer membrane porin F	A	340	Escherichia coli (strain K12)	Mutation(s): 0  Gene Names: ompF
UniProt
Find proteins for P02931 (Escherichia coli (strain K12)) Explore P02931  Go to UniProtKB:  P02931

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BCN	C [auth A]	BICINE C6 H13 N O4 FSVCELGFZIQNCK-UHFFFAOYSA-N
ZN (Subject of Investigation/LOI)	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free:  0.278 (Depositor), 0.278 (DCC) 
• R-Value Work:  0.195 (Depositor), 0.195 (DCC) 
• R-Value Observed: 0.199 (Depositor) 

Space Group: P 3 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 136.99	α = 90
b = 136.99	β = 90
c = 49.66	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data scaling
XDS	data reduction
MOLREP	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
Not funded	Korea, Republic Of	2019R1C1C1003863

Revision History  

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