3MTI | pdb_00003mti

The Crystal Structure of a rRNA Methylase from Streptococcus thermophilus to 1.95A

• PDB DOI: https://doi.org/10.2210/pdb3MTI/pdb

• Classification: TRANSFERASE
• Organism(s): Streptococcus thermophilus LMG 18311
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2010-04-30 Released: 2010-05-12 
• Deposition Author(s): Stein, A.J., Mulligan, R., Freeman, L., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 
  0.272 (Depositor), 0.280 (DCC) 
• R-Value Work: 
  0.238 (Depositor), 0.250 (DCC) 
• R-Value Observed: 
  0.240 (Depositor) 

Literature

The Crystal Structure of a rRNA Methylase from Streptococcus thermophilus to 1.95A

Stein, A.J., Mulligan, R., Freeman, L., 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: 41.99 kDa 
• Atom Count: 2,792 
• Modeled Residue Count: 346 
• Deposited Residue Count: 370 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
rRNA methylase	A, B	185	Streptococcus thermophilus LMG 18311	Mutation(s): 0  Gene Names: stu1645
UniProt
Find proteins for Q5M2Z6 (Streptococcus thermophilus (strain ATCC BAA-250 / LMG 18311)) Explore Q5M2Z6  Go to UniProtKB:  Q5M2Z6

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free:  0.272 (Depositor), 0.280 (DCC) 
• R-Value Work:  0.238 (Depositor), 0.250 (DCC) 
• R-Value Observed: 0.240 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.331	α = 90
b = 57.044	β = 109.11
c = 75.365	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
SBC-Collect	data collection
HKL-3000	data reduction
HKL-3000	data scaling
SHELX	phasing
MLPHARE	phasing
DM	phasing
ARP/wARP	model building
Coot	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-05-12 
Deposition Author(s): Stein, A.J., Mulligan, R., Freeman, L., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2010-05-12
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-11-08
  Changes: Refinement description
• Version 1.3: 2024-11-20
  Changes: Data collection, Database references, Derived calculations, Structure summary