2ZUL | pdb_00002zul

Crystal structure of Thermus thermophilus 16S rRNA methyltransferase RsmC (TTHA0533) in complex with cofactor S-adenosyl-L-Methionine

• PDB DOI: https://doi.org/10.2210/pdb2ZUL/pdb

• Classification: TRANSFERASE
• Organism(s): Thermus thermophilus HB8
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-10-21 Released: 2009-10-27 
• Deposition Author(s): Wang, H., Kawazoe, M., Tatsuguchi, A., Naoe, C., Takemoto, C., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.217 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.183 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.183 (Depositor) 

Literature

Crystal structure of Thermus thermophilus 16S rRNA methyltransferase RsmC (TTHA0533) in complex with cofactor S-adenosyl-L-Methionine

Wang, H., Kawazoe, M., Tatsuguchi, A., Naoe, C., Takemoto, C., Yokoyama, S.

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: 41.11 kDa 
• Atom Count: 3,173 
• Modeled Residue Count: 372 
• Deposited Residue Count: 375 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable ribosomal RNA small subunit methyltransferase	A	375	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for Q5SKW0 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SKW0  Go to UniProtKB:  Q5SKW0

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.217 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.183 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.183 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.852	α = 90
b = 80.072	β = 90
c = 93.632	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-10-27 
Deposition Author(s): Wang, H., Kawazoe, M., Tatsuguchi, A., Naoe, C., Takemoto, C., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History  

• Version 1.0: 2009-10-27
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.2: 2024-03-13
  Changes: Data collection, Database references, Derived calculations