4X5O | pdb_00004x5o

Human histidine tRNA synthetase

• PDB DOI: https://doi.org/10.2210/pdb4X5O/pdb

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


• Deposited: 2014-12-05 Released: 2015-11-25 
• Deposition Author(s): Kim, Y.K., Jeon, Y.H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 
  0.314 (Depositor), 0.270 (DCC) 
• R-Value Work: 
  0.248 (Depositor), 0.250 (DCC) 
• R-Value Observed: 
  0.252 (Depositor) 

Starting Model: experimental

Re-refinement Note

A newer entry is available that reflects an alternative modeling of the original data: 6O76

Literature

Structural characteristics of human histidyl-tRNA synthetase

Kim, Y.K., Chang, J.E., Kim, S., Jeon, Y.H.

(2015) Korean Soc Struct Biology 2: 142-148

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: 114.98 kDa 
• Atom Count: 6,256 
• Modeled Residue Count: 784 
• Deposited Residue Count: 1,018 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Histidine--tRNA ligase, cytoplasmic	A, B	509	Homo sapiens	Mutation(s): 0  Gene Names: HARS, HRS EC: 6.1.1.21
UniProt & NIH Common Fund Data Resources
Find proteins for P12081 (Homo sapiens) Explore P12081  Go to UniProtKB:  P12081
PHAROS:  P12081 GTEx:  ENSG00000170445

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free:  0.314 (Depositor), 0.270 (DCC) 
• R-Value Work:  0.248 (Depositor), 0.250 (DCC) 
• R-Value Observed: 0.252 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 97.669	α = 90
b = 97.669	β = 90
c = 254.409	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-11-25 
Deposition Author(s): Kim, Y.K., Jeon, Y.H.

Revision History  

• Version 1.0: 2015-11-25
  Type: Initial release
  
• Version 1.1: 2020-02-05
  Changes: Data collection, Derived calculations
• Version 1.2: 2023-11-08
  Changes: Data collection, Database references, Refinement description