2YWQ

Crystal structure of Thermus thermophilus Protein Y N-terminal domain

• PDB DOI: https://doi.org/10.2210/pdb2YWQ/pdb

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


• Deposited: 2007-04-21 Released: 2008-04-15 
• Deposition Author(s): Kawazoe, M., Takemoto, C., Kaminishi, T., Tatsuguchi, A., Saito, Y., Shirouzu, M., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.64 Å
• R-Value Free: 0.294 
• R-Value Work: 0.238 
• R-Value Observed: 0.238 

Literature

Crystal structure of Thermus thermophilus Protein Y N-terminal domain

Kawazoe, M., Takemoto, C., Kaminishi, T., Tatsuguchi, A., Saito, Y., Shirouzu, M., 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)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

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

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly 4  

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

Biological assembly 4 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 49.02 kDa 
• Atom Count: 2,908 
• Modelled Residue Count: 357 
• Deposited Residue Count: 420 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribosomal subunit interface protein	A, B, C, D	105	Thermus thermophilus HB8	Mutation(s): 0  Gene Names: TTHA1294
UniProt
Find proteins for Q5SIS0 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SIS0  Go to UniProtKB:  Q5SIS0

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.64 Å
• R-Value Free: 0.294 
• R-Value Work: 0.238 
• R-Value Observed: 0.238 
• Space Group: P 4₃ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.774	α = 90
b = 81.774	β = 90
c = 136.553	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-04-15 
Deposition Author(s): Kawazoe, M., Takemoto, C., Kaminishi, T., Tatsuguchi, A., Saito, Y., Shirouzu, M., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History  

• Version 1.0: 2008-04-15
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.2: 2024-10-16
  Changes: Data collection, Database references, Derived calculations, Structure summary