4BWA

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

• PDB DOI: https://doi.org/10.2210/pdb4BWA/pdb

• Classification: LIGASE
• Organism(s): Methanosarcina mazei
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2013-07-01 Released: 2013-07-31 
• Deposition Author(s): Schneider, S., Vrabel, M., Gattner, M.J., Fluegel, V., Lopez-Carillo, V., Carell, T.

---

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 

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

• PubMed: 24027216 
• 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). [e-mail].

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: 34.22 kDa 
• Atom Count: 2,169 
• Modelled Residue Count: 260 
• Deposited Residue Count: 291 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PYRROLYSINE--TRNA LIGASE	A	291	Methanosarcina mazei	Mutation(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

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
N0B	C [auth A]	Adenylated Norbornene C25 H36 N7 O10 P MYIVZOBPRNLOTH-PEZDGLODSA-M
PEG	D [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
EDO	E [auth A], F [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
MG	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 = 104.8	α = 90
b = 104.8	β = 90
c = 72.86	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-07-31 
Deposition Author(s): Schneider, S., Vrabel, M., Gattner, M.J., Fluegel, V., Lopez-Carillo, V., Carell, T.

Revision History  

• 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