8ZNA | pdb_00008zna

Myxococcus xanthus RomX

PDB DOI: https://doi.org/10.2210/pdb8ZNA/pdb

Classification: SIGNALING PROTEIN
Organism(s): Myxococcus xanthus DK 1622
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2024-05-26 Released: 2025-06-04
Deposition Author(s): Chakraborty, S., Gayathri, P.
Funding Organization(s): Department of Science & Technology (DST, India)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.89 Å
R-Value Free:
0.231 (Depositor), 0.240 (DCC)
R-Value Work:
0.190 (Depositor), 0.200 (DCC)
R-Value Observed:
0.192 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

RomX, a novel prokaryotic regulator, links the response receiver domain of RomR with GTP-bound MglA for establishing Myxococcus xanthus polarity

Chakraborty, S., Gayathri, P.

To be published.

Macromolecule Content

Total Structure Weight: 11.48 kDa
Atom Count: 863
Modeled Residue Count: 93
Deposited Residue Count: 95
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RomX	A	95	Myxococcus xanthus DK 1622	Mutation(s): 0 Gene Names: MXAN_3350
UniProt
Find proteins for Q1D725 (Myxococcus xanthus (strain DK1622)) Explore Q1D725 Go to UniProtKB: Q1D725
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q1D725
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EDO (Subject of Investigation/LOI) Query on EDO Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.89 Å
R-Value Free: 0.231 (Depositor), 0.240 (DCC)
R-Value Work: 0.190 (Depositor), 0.200 (DCC)
R-Value Observed: 0.192 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 33.295	α = 90
b = 56.076	β = 90
c = 68.616	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
MOSFLM	data reduction
Aimless	data scaling
AutoSol	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2025-06-04

Deposition Author(s):

Chakraborty, S.

Funding Organization	Location	Grant Number
Department of Science & Technology (DST, India)	India	CEFIPRA 5803-B

Revision History (Full details and data files)

Version 1.0: 2025-06-04
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.