6X94 | pdb_00006x94

An orthogonal seryl-tRNA synthetase/tRNA pair for noncanonical amino acid mutagenesis in Escherichia coli

• PDB DOI: https://doi.org/10.2210/pdb6X94/pdb

• Classification: LIGASE
• Organism(s): Methanosarcina mazei Go1
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2020-06-02 Released: 2020-11-04 
• Deposition Author(s): Zambaldo, C., Koh, M., Nasertorabi, F., Han, G.W., Chatterjee, A., Stevens, R.C., Schultz, P.G.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free: 
  0.169 (Depositor), 0.170 (DCC) 
• R-Value Work: 
  0.144 (Depositor), 0.140 (DCC) 
• R-Value Observed: 
  0.145 (Depositor) 

Starting Model: experimental

Literature

An orthogonal seryl-tRNA synthetase/tRNA pair for noncanonical amino acid mutagenesis in Escherichia coli.

Zambaldo, C., Koh, M., Nasertorabi, F., Han, G.W., Chatterjee, A., Stevens, R.C., Schultz, P.G.

(2020) Bioorg Med Chem 28: 115662-115662

• PubMed: 33069069 
• DOI: https://doi.org/10.1016/j.bmc.2020.115662
• Primary Citation of Related Structures:  
  6X94


• PubMed Abstract: 
  

  We report the development of the orthogonal amber-suppressor pair Archaeoglobus fulgidus seryl-tRNA (Af-tRNA ^Ser )/Methanosarcina mazei seryl-tRNA synthetase (MmSerRS) in Escherichia coli. Furthermore, the crystal structure of MmSerRS was solved at 1.45 Å resolution, which should enable structure-guided engineering of its active site to genetically encode small, polar noncanonical amino acids (ncAAs).

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Organizational Affiliation: 
• Department of Chemistry and Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 N. Torrey Pines Road, La Jolla, CA 92037, United States.
Departments of Biological Sciences and Chemistry, Bridge Institute, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, CA 90089, United States.
Department of Chemistry, Boston College, 2609 Beacon Street, 246B Merkert Chemistry Center, Chestnut Hill, MA 02467, United States. Electronic address: [e-mail].
Departments of Biological Sciences and Chemistry, Bridge Institute, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, CA 90089, United States. Electronic address: [e-mail].
Department of Chemistry and Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 N. Torrey Pines Road, La Jolla, CA 92037, United States. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 49.85 kDa 
• Atom Count: 4,216 
• Modeled Residue Count: 413 
• Deposited Residue Count: 426 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Serine--tRNA ligase	A	426	Methanosarcina mazei Go1	Mutation(s): 4  Gene Names: serS, MM_0865 EC: 6.1.1.11
UniProt
Find proteins for Q8PYJ6 (Methanosarcina mazei (strain ATCC BAA-159 / DSM 3647 / Goe1 / Go1 / JCM 11833 / OCM 88)) Explore Q8PYJ6  Go to UniProtKB:  Q8PYJ6

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SSA (Subject of Investigation/LOI)	B [auth A]	5'-O-(N-(L-SERYL)-SULFAMOYL)ADENOSINE C13 H19 N7 O8 S HQXFJGONGJPTLZ-YTMOPEAISA-N
PEG	C [auth A], D [auth A], E [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
DMS	F [auth A]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N
SCN	G [auth A], H [auth A], I [auth A], J [auth A], K [auth A]	THIOCYANATE ION C N S ZMZDMBWJUHKJPS-UHFFFAOYSA-M
K	L [auth A]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N
CL	M [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free:  0.169 (Depositor), 0.170 (DCC) 
• R-Value Work:  0.144 (Depositor), 0.140 (DCC) 
• R-Value Observed: 0.145 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.782	α = 90
b = 159.415	β = 90
c = 84.004	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
SCALA	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-11-04 
Deposition Author(s): Zambaldo, C., Koh, M., Nasertorabi, F., Han, G.W., Chatterjee, A., Stevens, R.C., Schultz, P.G.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01 - GM062159

Revision History  

• Version 1.0: 2020-11-04
  Type: Initial release
  
• Version 1.1: 2023-10-18
  Changes: Data collection, Database references, Refinement description