3ZXI

Crystal structure of human mitochondrial tyrosyl-tRNA synthetase in complex with a tyrosyl-adenylate analog

• PDB DOI: https://doi.org/10.2210/pdb3ZXI/pdb

• Classification: LIGASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2011-08-11 Released: 2011-11-16 
• Deposition Author(s): Bonnefond, L., Frugier, M., Rudinger-Thirion, J., Balg, C., Chenevert, R., Lorber, B., Giege, R., Sauter, C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.75 Å
• R-Value Free: 0.307 
• R-Value Work: 0.224 
• R-Value Observed: 0.228 

Starting Model: experimental

Literature

Exploiting Protein Engineering and Crystal Polymorphism for Successful X-Ray Structure Determination

Bonnefond, L., Schellenberger, P., Basquin, J., Demangeat, G., Ritzenthaler, C., Chenevert, R., Balg, C., Frugier, M., Rudinger-Thirion, J., Giege, R., Lorber, B., Sauter, C.

(2011) Cryst Growth Des 11: 4334

• DOI: https://doi.org/10.1021/CG101468P

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: 80.92 kDa 
• Atom Count: 4,928 
• Modelled Residue Count: 612 
• Deposited Residue Count: 712 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
TYROSYL-TRNA SYNTHETASE, MITOCHONDRIAL	A, B	356	Homo sapiens	Mutation(s): 0  EC: 6.1.1.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y2Z4 (Homo sapiens) Explore Q9Y2Z4  Go to UniProtKB:  Q9Y2Z4
GTEx:  ENSG00000139131

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TYA	C [auth A], D [auth B]	PHOSPHORIC ACID 2-AMINO-3-(4-HYDROXY-PHENYL)-PROPYL ESTER ADENOSIN-5'YL ESTER C19 H24 N6 O8 P JJLCVHBFTXDJMM-KFAHYOAQSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.75 Å
• R-Value Free: 0.307 
• R-Value Work: 0.224 
• R-Value Observed: 0.228 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.14	α = 90
b = 62.87	β = 90
c = 196.32	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-11-16 
Deposition Author(s): Bonnefond, L., Frugier, M., Rudinger-Thirion, J., Balg, C., Chenevert, R., Lorber, B., Giege, R., Sauter, C.

Revision History  

• Version 1.0: 2011-11-16
  Type: Initial release
  
• Version 1.1: 2019-03-06
  Changes: Data collection, Experimental preparation, Other
• Version 1.2: 2019-05-08
  Changes: Data collection, Experimental preparation
• Version 1.3: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description