4BWA

PylRS Y306G, Y384F, I405R mutant in complex with adenylated norbornene

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.184 

Starting Model: experimental
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This is version 1.3 of the entry. See complete history. 


Literature

Structural Insights Into Incorporation of Norbornene Amino Acids for Click Modification of Proteins

Schneider, S., Gattner, M.J., Vrabel, M., Flugel, V., Lopez-Carrillo, V., Prill, S., Carell, T.

(2013) Chembiochem 14: 2114

  • DOI: https://doi.org/10.1002/cbic.201300435
  • Primary Citation of Related Structures:  
    4BW9, 4BWA

  • PubMed Abstract: 

    Three for two: by using a Methanosarcina mazei PylRS triple mutant (Y306G, Y384F, I405R) the incorporation of two new exo-norbornene-containing pyrrolysine analogues was achieved. X-ray crystallographic analysis led to the identification of the crucial structural elements involved in substrate recognition by the evolved synthetase.

    • Organizational Affiliation: 

    Department of Chemistry, TU Munich, Lichtenbergstrasse 4, 85748 Garching (Germany). [email protected].


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
PYRROLYSINE--TRNA LIGASE291Methanosarcina mazeiMutation(s): 3 
EC: 6.1.1.26
UniProt
Find proteins for Q8PWY1 (Methanosarcina mazei (strain ATCC BAA-159 / DSM 3647 / Goe1 / Go1 / JCM 11833 / OCM 88))
Explore Q8PWY1 
Go to UniProtKB:  Q8PWY1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8PWY1
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
N0B
Query on N0B
Download Ideal Coordinates CCD File 
C [auth A]Adenylated Norbornene
C25 H36 N7 O10 P
MYIVZOBPRNLOTH-PEZDGLODSA-M
PEG
Query on PEG
Download Ideal Coordinates CCD File 
D [auth A]DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
EDO
Query on EDO
Download Ideal Coordinates CCD File 
E [auth A],
F [auth A]		1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
MG
Query on MG
Download Ideal Coordinates CCD File 
B [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.184 
  • Space Group: P 64
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 104.8α = 90
b = 104.8β = 90
c = 72.86γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-07-31
    Type: Initial release
  • Version 1.1: 2013-09-25
    Changes: Database references
  • Version 1.2: 2013-12-25
    Changes: Database references
  • Version 1.3: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description