2DYI | pdb_00002dyi

Crystal structure of 16S ribosomal RNA processing protein RimM from Thermus thermophilus HB8

• PDB DOI: https://doi.org/10.2210/pdb2DYI/pdb

• Classification: RIBOSOME
• Organism(s): Thermus thermophilus HB8
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2006-09-14 Released: 2007-03-14 
• Deposition Author(s): Kawazoe, M., Takemoto, C., Kaminishi, T., Tatsuguchi, A., Shirouzu, M., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.256 (Depositor), 0.256 (DCC) 
• R-Value Work: 
  0.192 (Depositor), 0.192 (DCC) 
• R-Value Observed: 
  0.192 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of 16S ribosomal RNA processing protein RimM from Thermus thermophilus HB8

Kawazoe, M., Takemoto, C., Kaminishi, T., Tatsuguchi, A., Shirouzu, M., Yokoyama, S.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 18.09 kDa 
• Atom Count: 1,417 
• Modeled Residue Count: 162 
• Deposited Residue Count: 162 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable 16S rRNA-processing protein rimM	A	162	Thermus thermophilus HB8	Mutation(s): 0  Gene Names: TTHA1033
UniProt
Find proteins for Q5SJH5 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SJH5  Go to UniProtKB:  Q5SJH5

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.256 (Depositor), 0.256 (DCC) 
• R-Value Work:  0.192 (Depositor), 0.192 (DCC) 
• R-Value Observed: 0.192 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.328	α = 90
b = 53.103	β = 90
c = 70.437	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-03-14 
Deposition Author(s): Kawazoe, M., Takemoto, C., Kaminishi, T., Tatsuguchi, A., Shirouzu, M., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History  

• Version 1.0: 2007-03-14
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.3: 2024-03-13
  Changes: Data collection, Database references
• Version 1.4: 2024-04-03
  Changes: Refinement description