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

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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:

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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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

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Ligand Structure Quality Assessment

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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

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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.