3ONP | pdb_00003onp

Crystal Structure of tRNA/rRNA Methyltransferase SpoU from Rhodobacter sphaeroides

• PDB DOI: https://doi.org/10.2210/pdb3ONP/pdb

• Classification: TRANSFERASE
• Organism(s): Cereibacter sphaeroides 2.4.1
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2010-08-30 Released: 2010-09-08 
• Deposition Author(s): Kim, Y., Tesar, C., Jedrzejczak, R., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.219 (Depositor), 0.216 (DCC) 
• R-Value Work: 
  0.189 (Depositor), 0.189 (DCC) 
• R-Value Observed: 
  0.191 (Depositor) 

Literature

Crystal Structure of tRNA/rRNA Methyltransferase SpoU from Rhodobacter sphaeroides

Kim, Y., Tesar, C., Jedrzejczak, R., Joachimiak, A.

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 and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 28.65 kDa 
• Atom Count: 1,486 
• Modeled Residue Count: 159 
• Deposited Residue Count: 249 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
tRNA/rRNA methyltransferase (SpoU)	A	249	Cereibacter sphaeroides 2.4.1	Mutation(s): 0  Gene Names: RHOS4_30450, RSP_3829 EC: 2.1.1.200
UniProt
Find proteins for Q3IXX1 (Cereibacter sphaeroides (strain ATCC 17023 / DSM 158 / JCM 6121 / CCUG 31486 / LMG 2827 / NBRC 12203 / NCIMB 8253 / ATH 2.4.1.)) Explore Q3IXX1  Go to UniProtKB:  Q3IXX1

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	D [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
BME	C [auth A], F [auth A]	BETA-MERCAPTOETHANOL C2 H6 O S DGVVWUTYPXICAM-UHFFFAOYSA-N
ACY	B [auth A], G [auth A]	ACETIC ACID C2 H4 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-N
CL	E [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

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: 1.90 Å
• R-Value Free:  0.219 (Depositor), 0.216 (DCC) 
• R-Value Work:  0.189 (Depositor), 0.189 (DCC) 
• R-Value Observed: 0.191 (Depositor) 

Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.782	α = 90
b = 74.782	β = 90
c = 139.105	γ = 120

Software Package:

Software Name	Purpose
SBC-Collect	data collection
HKL-3000	data collection
HKL-3000	phasing
SHELXS	phasing
MLPHARE	phasing
RESOLVE	model building
SOLVE	phasing
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
RESOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-09-08 
Deposition Author(s): Kim, Y., Tesar, C., Jedrzejczak, R., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2010-09-08
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2025-03-26
  Changes: Data collection, Database references, Derived calculations, Structure summary