9J9N | pdb_00009j9n

artificial mononuclear Zn-bound metalloprotein 2 (M2:Zn)

PDB DOI: https://doi.org/10.2210/pdb9J9N/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

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.86 Å
R-Value Free:
0.250 (Depositor), 0.254 (DCC)
R-Value Work:
0.194 (Depositor), 0.198 (DCC)
R-Value Observed:
0.197 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

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

Jeong, W.J., Song, W.J.

To be published.

Macromolecule Content

Total Structure Weight: 74.28 kDa
Atom Count: 5,052
Modeled Residue Count: 662
Deposited Residue Count: 680
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P02931
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN (Subject of Investigation/LOI) Query on ZN Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth B]	C [auth A], D [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.86 Å
R-Value Free: 0.250 (Depositor), 0.254 (DCC)
R-Value Work: 0.194 (Depositor), 0.198 (DCC)
R-Value Observed: 0.197 (Depositor)

Space Group: P 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 136.12	α = 90
b = 136.12	β = 90
c = 48.88	γ = 120

Software Package:

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

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2025-07-02

Deposition Author(s):

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

Revision History (Full details and data files)

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

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.