2EL7 | pdb_00002el7

Crystal structure of Tryptophanyl-tRNA synthetase from Thermus thermophilus

• PDB DOI: https://doi.org/10.2210/pdb2EL7/pdb

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


• Deposited: 2007-03-26 Released: 2008-03-18 
• Deposition Author(s): Yanagisawa, T., Sumida, T., Ishii, R., Sekine, S., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.267 (Depositor), 0.270 (DCC) 
• R-Value Work: 
  0.195 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.195 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of Tryptophanyl-tRNA synthetase from Thermus thermophilus

Yanagisawa, T., Sumida, T., Ishii, R., Sakamoto, K., Shirouzu, M., Sekine, S., Shinkai, A., Kuramitsu, S., Yokoyama, S.

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: 76.17 kDa 
• Atom Count: 5,269 
• Modeled Residue Count: 634 
• Deposited Residue Count: 674 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tryptophanyl-tRNA synthetase	A, B	337	Thermus thermophilus HB8	Mutation(s): 0  Gene Names: trpS EC: 6.1.1.2
UniProt
Find proteins for Q5SIY7 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SIY7  Go to UniProtKB:  Q5SIY7

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	C [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.267 (Depositor), 0.270 (DCC) 
• R-Value Work:  0.195 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.195 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.318	α = 90
b = 72.488	β = 90
c = 229.72	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-03-18 
Deposition Author(s): Yanagisawa, T., Sumida, T., Ishii, R., Sekine, S., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History  

• Version 1.0: 2008-03-18
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.2: 2023-10-25
  Changes: Data collection, Database references, Derived calculations, Refinement description