5Y06 | pdb_00005y06

Structural characterization of msmeg_4306 from Mycobacterium smegmatis

• PDB DOI: https://doi.org/10.2210/pdb5Y06/pdb

• Classification: UNKNOWN FUNCTION
• Organism(s): Mycolicibacterium smegmatis MC2 155
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2017-07-14 Released: 2018-05-02 
• Deposition Author(s): Kumar, A., Karthikeyan, S.
• Funding Organization(s): CSIR, Government of India

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.61 Å
• R-Value Free: 
  0.271 (Depositor), 0.276 (DCC) 
• R-Value Work: 
  0.240 (Depositor), 0.242 (DCC) 
• R-Value Observed: 
  0.242 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of the MSMEG_4306 gene product from Mycobacterium smegmatis

Kumar, A., Karthikeyan, S.

(2018) Acta Crystallogr F Struct Biol Commun 74: 166-173

• PubMed: 29497021 
• DOI: https://doi.org/10.1107/S2053230X18002236
• Primary Citation Related Structures: 
  5Y05, 5Y06


• PubMed Abstract: 
  

  The MSMEG_4306 gene from Mycobacterium smegmatis encodes a protein of unknown function with 242 amino-acid residues that contains a conserved zinc-ribbon domain at its C-terminus. Here, the crystal structure of MSMEG_4306 determined by the single-wavelength anomalous dispersion method using just one zinc ion co-purified with the protein is reported. The crystal structure of MSMEG_4306 shows a coiled-coil helix domain in the N-terminal region and a zinc-ribbon domain in the C-terminal region. A structural similarity search against the Protein Data Bank using MSMEG_4306 as a query revealed two similar structures, namely CT398 from Chlamydia trachomatis and HP0958 from Helicobacter pylori, although they share only ∼15% sequence identity with MSMEG_4306. Based on comparative analysis, it is predicted that MSMEG_4306 may be involved in secretion systems, possibly by interacting with multiple proteins or nucleic acids.

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Organizational Affiliation: 
• CSIR - Institute of Microbial Technology, Council of Scientific and Industrial Research (CSIR), Sector 39A, Chandigarh 160 036, India.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 29.7 kDa 
• Atom Count: 1,753 
• Modeled Residue Count: 235 
• Deposited Residue Count: 262 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
msmeg_4306	A	262	Mycolicibacterium smegmatis MC2 155	Mutation(s): 0  Gene Names: MSMEG_4306
UniProt
Find proteins for A0R095 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)) Explore A0R095  Go to UniProtKB:  A0R095

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	B [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN (Subject of Investigation/LOI)	C [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.61 Å
• R-Value Free:  0.271 (Depositor), 0.276 (DCC) 
• R-Value Work:  0.240 (Depositor), 0.242 (DCC) 
• R-Value Observed: 0.242 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.6	α = 90
b = 76.6	β = 90
c = 84.811	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
iMOSFLM	data reduction
Aimless	data scaling
PHENIX	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2018-05-02 
Deposition Author(s): Kumar, A., Karthikeyan, S.

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Funding Organization	Location	Grant Number
CSIR, Government of India	India	BSC0104, BSC0210

Revision History  

• Version 1.0: 2018-05-02
  Type: Initial release
  
• Version 1.1: 2023-11-22
  Changes: Data collection, Database references, Refinement description