9J9M | pdb_00009j9m

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

PDB DOI: https://doi.org/10.2210/pdb9J9M/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: 2.29 Å
R-Value Free:
0.221 (Depositor), 0.227 (DCC)
R-Value Work:
0.182 (Depositor), 0.191 (DCC)
R-Value Observed:
0.184 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.1 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: 74.17 kDa
Atom Count: 5,434
Modeled Residue Count: 678
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
MN (Subject of Investigation/LOI) Query on MN 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]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-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: 2.29 Å
R-Value Free: 0.221 (Depositor), 0.227 (DCC)
R-Value Work: 0.182 (Depositor), 0.191 (DCC)
R-Value Observed: 0.184 (Depositor)

Space Group: P 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 136.81	α = 90
b = 136.81	β = 90
c = 50.067	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
Version 1.1: 2025-11-12
Changes: Source and taxonomy

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.