2ZBR

Crystal structure of ribosomal protein L11 methyltransferase from Thermus thermophilus in complex with S-adenosyl-ornithine

• PDB DOI: https://doi.org/10.2210/pdb2ZBR/pdb

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


• Deposited: 2007-10-26 Released: 2008-11-11 
• Deposition Author(s): Kaminishi, T., Sakai, H., Takemoto-Hori, C., Terada, T., Nakagawa, N., Maoka, N., Kuramitsu, S., Shirouzu, M., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.247 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.224 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.224 (Depositor) 

Literature

Crystal structure of ribosomal protein L11 methyltransferase from Thermus thermophilus

Kaminishi, T., Sakai, H., Takemoto-Hori, C., Terada, T., Nakagawa, N., Maoka, N., Kuramitsu, S., Shirouzu, M., Yokoyama, S.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 28.04 kDa 
• Atom Count: 2,124 
• Modelled Residue Count: 248 
• Deposited Residue Count: 254 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribosomal protein L11 methyltransferase	A	254	Thermus thermophilus	Mutation(s): 0  Gene Names: prmA EC: 2.1.1
UniProt
Find proteins for Q84BQ9 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q84BQ9  Go to UniProtKB:  Q84BQ9

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SFG	B [auth A]	SINEFUNGIN C15 H23 N7 O5 LMXOHSDXUQEUSF-YECHIGJVSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.247 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.224 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.224 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 82.279	α = 90
b = 75.48	β = 130.67
c = 62.042	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-11-11 
Deposition Author(s): Kaminishi, T., Sakai, H., Takemoto-Hori, C., Terada, T., Nakagawa, N., Maoka, N., Kuramitsu, S., Shirouzu, M., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History  

• Version 1.0: 2008-11-11
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.2: 2024-03-13
  Changes: Data collection, Database references, Derived calculations