4HPW

Crystal structure of Tyrosine-tRNA ligase mutant complexed with unnatural amino acid 3-o-methyl-Tyrosine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.200 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Crystal structure of Tyrosine-tRNA ligase mutant complexed with unnatural amino acid 3-o-methyl-Tyrosine

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.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Tyrosine--tRNA ligase310Methanocaldococcus jannaschii DSM 2661Mutation(s): 6 
Gene Names: tyrSMJ0389
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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ57834
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
3YM
Query on 3YM

Download Ideal Coordinates CCD File 
B [auth A]3-methoxy-L-tyrosine
C10 H13 N O4
PFDUUKDQEHURQC-ZETCQYMHSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.200 
  • Space Group: P 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 52.629α = 90
b = 38.83β = 90.75
c = 82.957γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
CNSrefinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-10-30
    Type: Initial release
  • Version 1.1: 2015-05-27
    Changes: Structure summary
  • Version 1.2: 2019-07-17
    Changes: Data collection, Refinement description
  • Version 1.3: 2024-02-28
    Changes: Data collection, Database references, Derived calculations