3D6V

Crystal structure of 4-(trifluoromethyldiazirinyl)phenylalanyl-tRNA synthetase

• PDB DOI: https://doi.org/10.2210/pdb3D6V/pdb
• Entry: 3D6V supersedes: 2Q1I

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


• Deposited: 2008-05-20 Released: 2008-05-27 
• Deposition Author(s): Liu, W., Tippmann, E., Mack, A.V., Schultz, P.G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.270 
• R-Value Work: 0.193 
• R-Value Observed: 0.197 

Literature

A genetically encoded diazirine photocrosslinker in Escherichia coli

Tippmann, E., Liu, W., Summerer, D., Mack, A.V., Schultz, P.G.

(2007) Chembiochem 8: 2210-2214

• PubMed: 18000916 
• DOI: https://doi.org/10.1002/cbic.200700460
• Primary Citation of Related Structures:  
  3D6U, 3D6V

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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: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 36.42 kDa 
• Atom Count: 2,689 
• Modelled Residue Count: 308 
• Deposited Residue Count: 314 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tyrosyl-tRNA synthetase	A	314	Methanocaldococcus jannaschii	Mutation(s): 7  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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TFQ	B [auth A]	4-(2,2,2-TRIFLUOROETHYL)-L-PHENYLALANINE C11 H12 F3 N O2 VXIZYDKGLBPCAQ-VIFPVBQESA-N
BME	C [auth A]	BETA-MERCAPTOETHANOL C2 H6 O S DGVVWUTYPXICAM-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.270 
• R-Value Work: 0.193 
• R-Value Observed: 0.197 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 104.155	α = 90
b = 104.155	β = 90
c = 70.826	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-05-27 
Deposition Author(s): Liu, W., Tippmann, E., Mack, A.V., Schultz, P.G.
• This entry supersedes: 2Q1I

Revision History  

• Version 1.0: 2008-05-27
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2021-10-20
  Changes: Database references, Derived calculations
• Version 1.3: 2024-02-21
  Changes: Data collection