1WOY

Crystal structure of methionyl tRNA synthetase Y225F mutant from Thermus thermophilus

• PDB DOI: https://doi.org/10.2210/pdb1WOY/pdb

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


• Deposited: 2004-08-27 Released: 2005-09-13 
• Deposition Author(s): Konno, M., Takeda, R., Nureki, O., 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: 0.226 
• R-Value Work: 0.189 

Starting Model: experimental

Literature

Crystal structure of methionyl tRNA synthetase Y225F mutant from Thermus thermophilus

Konno, M., Takeda, R., Nureki, O., 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: 58.07 kDa 
• Atom Count: 4,452 
• Modelled Residue Count: 500 
• Deposited Residue Count: 500 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Methionyl-tRNA synthetase	A	500	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: 0.226 
• R-Value Work: 0.189 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.416	α = 90
b = 82.731	β = 90
c = 141.405	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: 2005-09-13 
Deposition Author(s): Konno, M., Takeda, R., Nureki, O., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History  

• Version 1.0: 2005-09-13
  Type: Initial release
  
• Version 1.1: 2007-10-05
  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