5IHX | pdb_00005ihx

Crystal Structure of a C-terminally truncated Aspergillus nidulans mitochondrial tyrosyl-tRNA synthetase

• PDB DOI: https://doi.org/10.2210/pdb5IHX/pdb

• Classification: LIGASE
• Organism(s): Aspergillus nidulans FGSC A4
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2016-02-29 Released: 2016-04-06 
• Deposition Author(s): Lamech, L.T., Lambowitz, A.M.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.216 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.180 (Depositor), 0.185 (DCC) 
• R-Value Observed: 
  0.182 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of a C-terminally truncated Aspergillus nidulans mitochondrial tyrosyl-tRNA synthetase

Lamech, L.T., Saoji, M., Paukstelis, P.J., Lambowitz, A.M.

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: 90.74 kDa 
• Atom Count: 5,643 
• Modeled Residue Count: 699 
• Deposited Residue Count: 790 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tyrosine--tRNA ligase, mitochondrial	A, B	395	Aspergillus nidulans FGSC A4	Mutation(s): 0  Gene Names: AN1709.2 EC: 6.1.1.1
UniProt
Find proteins for Q5BCM1 (Emericella nidulans (strain FGSC A4 / ATCC 38163 / CBS 112.46 / NRRL 194 / M139)) Explore Q5BCM1  Go to UniProtKB:  Q5BCM1

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TYR	C [auth A]	TYROSINE C9 H11 N O3 OUYCCCASQSFEME-QMMMGPOBSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.216 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.180 (Depositor), 0.185 (DCC) 
• R-Value Observed: 0.182 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.461	α = 90
b = 84.95	β = 90
c = 164.247	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data collection
HKL-2000	data scaling
PHASER	phasing
HKL-2000	data reduction

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2016-04-06 
Deposition Author(s): Lamech, L.T., Lambowitz, A.M.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM37951

Revision History  

• Version 1.0: 2016-04-06
  Type: Initial release
  
• Version 1.1: 2017-09-27
  Changes: Author supporting evidence, Derived calculations
• Version 1.2: 2019-12-25
  Changes: Author supporting evidence
• Version 1.3: 2023-09-27
  Changes: Data collection, Database references, Refinement description