7CMS | pdb_00007cms

Crystal structure of Tryptophanyl-tRNA synthetase from Bacillus stearothermophilus in complex with chuangxinmycin

• PDB DOI: https://doi.org/10.2210/pdb7CMS/pdb

• Classification: ANTIBIOTIC
• Organism(s): Geobacillus stearothermophilus
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2020-07-28 Released: 2021-08-04 
• Deposition Author(s): Lyu, G., Fan, S., Jin, Y., Zou, S., Wu, G., Yang, Z.
• Funding Organization(s): National Natural Science Foundation of China (NSFC), Ministry of Science and Technology (MoST, China)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.209 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.169 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.171 (Depositor) 

Starting Model: experimental

Literature

Structural insights into the specific interaction between Geobacillus stearothermophilus tryptophanyl-tRNA synthetase and antimicrobial Chuangxinmycin.

Fan, S., Lv, G., Feng, X., Wu, G., Jin, Y., Yan, M., Yang, Z.

(2022) J Biological Chem 298: 101580

• DOI: https://doi.org/10.1016/j.jbc.2022.101580

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)

Biological Assembly Evidence: isothermal titration calorimetry

Macromolecule Content 

• Total Structure Weight: 75.11 kDa 
• Atom Count: 5,711 
• Modeled Residue Count: 653 
• Deposited Residue Count: 656 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tryptophan--tRNA ligase	A, B	328	Geobacillus stearothermophilus	Mutation(s): 1  Gene Names: trpS EC: 6.1.1.2
UniProt
Find proteins for P00953 (Geobacillus stearothermophilus) Explore P00953  Go to UniProtKB:  P00953

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
9E0 (Subject of Investigation/LOI)	C [auth A], E [auth B]	(5~{S},6~{R})-5-methyl-7-thia-2-azatricyclo[6.3.1.0^{4,12}]dodeca-1(12),3,8,10-tetraene-6-carboxylic acid C12 H11 N O2 S DKHFLDXCKWDVMF-UPONEAKYSA-N
PO4 (Subject of Investigation/LOI)	D [auth A], F [auth B]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.209 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.169 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.171 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 91.675	α = 90
b = 91.675	β = 90
c = 152.37	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data scaling
PDB_EXTRACT	data extraction
HKL-2000	data reduction
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2021-08-04 
Deposition Author(s): Lyu, G., Fan, S., Jin, Y., Zou, S., Wu, G., Yang, Z.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	81761128016
National Natural Science Foundation of China (NSFC)	China	81621064
Ministry of Science and Technology (MoST, China)	China	2018YFA0901800

Revision History  

• Version 1.0: 2021-08-04
  Type: Initial release
  
• Version 1.1: 2022-02-16
  Changes: Database references
• Version 1.2: 2023-11-29
  Changes: Data collection, Refinement description