2EGV | pdb_00002egv

Crystal structure of rRNA methyltransferase with SAM ligand

• PDB DOI: https://doi.org/10.2210/pdb2EGV/pdb

• Classification: RNA methyltransferase
• Organism(s): Aquifex aeolicus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2007-03-02 Released: 2007-09-04 
• Deposition Author(s): Dong, X., Shirouzu, M., Bessho, Y., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free: 
  0.245 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.218 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.218 (Depositor) 

Literature

Crystal structure of rRNA methyltransferase with SAM ligand

Dong, X., Bessho, Y., Shirouzu, M., Yokoyama, S.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 54.25 kDa 
• Atom Count: 4,120 
• Modeled Residue Count: 458 
• Deposited Residue Count: 458 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UPF0088 protein aq_165	A, B	229	Aquifex aeolicus	Mutation(s): 0  Gene Names: RsmE EC: 2.1.1.193
UniProt
Find proteins for O66552 (Aquifex aeolicus (strain VF5)) Explore O66552  Go to UniProtKB:  O66552

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SAM	C [auth A], D [auth B]	S-ADENOSYLMETHIONINE C15 H22 N6 O5 S MEFKEPWMEQBLKI-FCKMPRQPSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free:  0.245 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.218 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.218 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.364	α = 90
b = 76.976	β = 90
c = 97.762	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-09-04 
Deposition Author(s): Dong, X., Shirouzu, M., Bessho, Y., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History  

• Version 1.0: 2007-09-04
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2024-03-13
  Changes: Data collection, Database references