2HGZ | pdb_00002hgz

Crystal structure of a p-benzoyl-L-phenylalanyl-tRNA synthetase

• PDB DOI: https://doi.org/10.2210/pdb2HGZ/pdb

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


• Deposited: 2006-06-27 Released: 2007-06-05 
• Deposition Author(s): Liu, W., Alfonta, L., Mack, A.V., Schultz, P.G.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.270 (Depositor), 0.276 (DCC) 
• R-Value Work: 
  0.210 (Depositor), 0.205 (DCC) 
• R-Value Observed: 
  0.217 (Depositor) 

Starting Model: experimental

Literature

Structural basis for the recognition of para-benzoyl-L-phenylalanine by evolved aminoacyl-tRNA synthetases.

Liu, W., Alfonta, L., Mack, A.V., Schultz, P.G.

(2007) Angew Chem Int Ed Engl 46: 6073-6075

• PubMed: 17628477 
• DOI: https://doi.org/10.1002/anie.200701990
• Primary Citation Related Structures: 
  2HGZ

---

Organizational Affiliation: 
• Department of Chemistry and the Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 N. Torrey Pines Rd, La Jolla, CA 92037, USA.

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,PQS (software)

Macromolecule Content 

• Total Structure Weight: 35.2 kDa 
• Atom Count: 2,602 
• Modeled Residue Count: 306 
• Deposited Residue Count: 306 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tyrosyl-tRNA synthetase	A	306	Methanocaldococcus jannaschii	Mutation(s): 3  Gene Names: tyrS 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
PBF	B [auth A]	PARA-(BENZOYL)-PHENYLALANINE C16 H15 N O3 TVIDEEHSOPHZBR-AWEZNQCLSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.270 (Depositor), 0.276 (DCC) 
• R-Value Work:  0.210 (Depositor), 0.205 (DCC) 
• R-Value Observed: 0.217 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 101.639	α = 90
b = 101.639	β = 90
c = 71.466	γ = 90

Software Package:

Software Name	Purpose
AMoRE	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-06-05 
Deposition Author(s): Liu, W., Alfonta, L., Mack, A.V., Schultz, P.G.

Revision History  

• Version 1.0: 2007-06-05
  Type: Initial release
  
• Version 1.1: 2008-02-06
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.3: 2021-10-20
  Changes: Database references, Derived calculations
• Version 1.4: 2024-02-14
  Changes: Data collection
• Version 1.5: 2024-04-03
  Changes: Refinement description