7JLZ | pdb_00007jlz

Crystal structure of 30S ribosomal A1408 methyltransferase from an uncultured bacterium (UncKam)

• PDB DOI: https://doi.org/10.2210/pdb7JLZ/pdb

• Classification: RNA BINDING PROTEIN
• Organism(s): uncultured bacterium
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2020-07-30 Released: 2021-08-04 
• Deposition Author(s): Nosrati, M., Conn, G.L.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.64 Å
• R-Value Free: 
  0.224 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.196 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.198 (Depositor) 

Starting Model: experimental

Literature

Roles of conserved tryptophans in substrate recognition and catalysis by the aminoglycoside-resistance 16S rRNA (m1A1408) rRNA methyltransferases

Nosrati, M., Witek, M.A., Dayne, W., Zelinskaya, N., Dunham, C.M., Conn, G.L.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 24.88 kDa 
• Atom Count: 1,783 
• Modeled Residue Count: 204 
• Deposited Residue Count: 214 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
16S rRNA methylase	A	214	uncultured bacterium	Mutation(s): 0  Gene Names: ACD_24C00409G0003
UniProt
Find proteins for A0ACD6B9R2 (uncultured bacterium) Explore A0ACD6B9R2  Go to UniProtKB:  A0ACD6B9R2

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	B [auth A], C [auth A], D [auth A], E [auth A], F [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.64 Å
• R-Value Free:  0.224 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.196 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.198 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.37	α = 90
b = 66.33	β = 90
c = 133.01	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
XDS	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2021-08-04 
Deposition Author(s): Nosrati, M., Conn, G.L.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	R01-AI088025

Revision History  

• Version 1.0: 2021-08-04
  Type: Initial release
  
• Version 1.1: 2023-10-18
  Changes: Data collection, Database references, Refinement description