4HK4

Crystal structure of apo Tyrosine-tRNA ligase mutant protein

• PDB DOI: https://doi.org/10.2210/pdb4HK4/pdb

• Classification: LIGASE
• Organism(s): Methanocaldococcus jannaschii
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2012-10-15 Released: 2013-04-17 
• Deposition Author(s): Yu, Y., Zhou, Q., Dong, J., Li, J., Xiaoxuan, L., Mukherjee, A., Ouyang, H., Nilges, M., Li, H., Gao, F., Gong, W., Lu, Y., Wang, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.277 
• R-Value Work: 0.229 
• R-Value Observed: 0.231 

Literature

Crystal structure of apo Tyrosine-tRNA ligase mutant protein

Yu, Y., Zhou, Q., Dong, J., Li, J., Xiaoxuan, L., Mukherjee, A., Ouyang, H., Nilges, M., Li, H., Gao, F., Gong, W., Lu, Y., Wang, J.

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: 35.85 kDa 
• Atom Count: 2,492 
• Modelled Residue Count: 309 
• Deposited Residue Count: 312 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tyrosine--tRNA ligase	A	312	Methanocaldococcus jannaschii	Mutation(s): 6  Gene Names: tyrS, MJ0389 EC: 6.1.1.1
UniProt
Find proteins for Q57834 (Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440)) Explore Q57834  Go to UniProtKB:  Q57834

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PEG	B [auth A], C [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.277 
• R-Value Work: 0.229 
• R-Value Observed: 0.231 
• Space Group: P 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.695	α = 90
b = 38.886	β = 90.98
c = 83.061	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-04-17 
Deposition Author(s): Yu, Y., Zhou, Q., Dong, J., Li, J., Xiaoxuan, L., Mukherjee, A., Ouyang, H., Nilges, M., Li, H., Gao, F., Gong, W., Lu, Y., Wang, J.

Revision History  

• Version 1.0: 2013-04-17
  Type: Initial release
  
• Version 1.1: 2013-07-10
  Changes: Structure summary
• Version 1.2: 2015-05-27
  Changes: Structure summary
• Version 1.3: 2017-11-15
  Changes: Refinement description
• Version 1.4: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description