3M4X | pdb_00003m4x

Structure of a ribosomal methyltransferase

• PDB DOI: https://doi.org/10.2210/pdb3M4X/pdb

• Classification: TRANSFERASE
• Organism(s): Enterococcus faecium
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2010-03-12 Released: 2010-04-14 
• Deposition Author(s): Galimand, M., Schmitt, E., Panvert, M., Mechulam, Y., Courvalin, P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.28 Å
• R-Value Free: 
  0.250 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.197 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.199 (Depositor) 

Starting Model: experimental

Literature

Structure of an RNA methyltransferase

Galimand, M., Schmitt, E., Panvert, M., Mechulam, Y., Courvalin, P.

To be published.

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: 51.75 kDa 
• Atom Count: 3,569 
• Modeled Residue Count: 440 
• Deposited Residue Count: 456 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NOL1/NOP2/sun family protein	A	456	Enterococcus faecium	Mutation(s): 0  Gene Names: EfmM EC: 2.1.1
UniProt
Find proteins for Q3Y1J9 (Enterococcus faecium (strain ATCC BAA-472 / TX0016 / DO)) Explore Q3Y1J9  Go to UniProtKB:  Q3Y1J9

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.28 Å
• R-Value Free:  0.250 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.197 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.199 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 98.556	α = 90
b = 98.556	β = 90
c = 106.061	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
PHASER	phasing
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-04-14 
Deposition Author(s): Galimand, M., Schmitt, E., Panvert, M., Mechulam, Y., Courvalin, P.

Revision History  

• Version 1.0: 2010-04-14
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.3: 2023-11-22
  Changes: Data collection
• Version 1.4: 2024-11-20
  Changes: Structure summary