5IJX | pdb_00005ijx

Crystal Structure of a C-terminally truncated Coccidioides posadasii mitochondrial tyrosyl-tRNA synthetase

• PDB DOI: https://doi.org/10.2210/pdb5IJX/pdb

• Classification: LIGASE
• Organism(s): Coccidioides posadasii C735 delta SOWgp
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2016-03-02 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: 2.63 Å
• R-Value Free: 
  0.236 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.206 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.208 (Depositor) 

Literature

Crystal Structure of a C-terminally truncated Coccidioides posadasii 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: 44.31 kDa 
• Atom Count: 2,828 
• Modeled Residue Count: 365 
• Deposited Residue Count: 384 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tyrosine--tRNA ligase, mitochondrial	A	384	Coccidioides posadasii C735 delta SOWgp	Mutation(s): 0  Gene Names: CPC735_063460 EC: 6.1.1.1
UniProt
Find proteins for C5P455 (Coccidioides posadasii (strain C735)) Explore C5P455  Go to UniProtKB:  C5P455

Small Molecules

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

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.63 Å
• R-Value Free:  0.236 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.206 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.208 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 117.173	α = 90
b = 75.785	β = 94.55
c = 52.316	γ = 90

Software Package:

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

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: 2020-03-04
  Changes: Data collection
• Version 1.4: 2024-11-13
  Changes: Data collection, Database references, Structure summary