2D54

Crystal Structure of Methionyl tRNA Synthetase Y225A Mutant from Thermus Thermophilus

• PDB DOI: https://doi.org/10.2210/pdb2D54/pdb

• Classification: ISOMERASE
• Organism(s): Thermus thermophilus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2005-10-28 Released: 2006-12-19 
• Deposition Author(s): Konno, M., Takeda, R., Takasaka, R., Mori, Y., Ishii, R., 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: 
  0.254 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.208 (Depositor), 0.210 (DCC) 

Starting Model: experimental

Literature

Y225F/Amutation for Met-tRNA synthetase reveals importance of hydrophobic circumstance

Konno, M., Takeda, R., Takasaka, R., Mori, Y., Ishii, R., 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: 58.19 kDa 
• Atom Count: 4,291 
• Modelled Residue Count: 500 
• Deposited Residue Count: 502 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Methionyl-tRNA synthetase	A	502	Thermus thermophilus	Mutation(s): 1  EC: 6.1.1.10
UniProt
Find proteins for P23395 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore P23395  Go to UniProtKB:  P23395

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.254 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.208 (Depositor), 0.210 (DCC) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.318	α = 90
b = 82.209	β = 90
c = 120.56	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-12-19 
Deposition Author(s): Konno, M., Takeda, R., Takasaka, R., Mori, Y., Ishii, R., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History  

• Version 1.0: 2006-12-19
  Type: Initial release
  
• Version 1.1: 2007-10-09
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2021-11-10
  Changes: Database references, Derived calculations
• Version 1.4: 2023-10-25
  Changes: Data collection, Refinement description