Independent saturation of three TrpRS subsites generates a partially-assembled state similar to those observed in molecular simulations

Experimental Data Snapshot

  • Resolution: 2.65 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.210 

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Independent saturation of three TrpRS subsites generates a partially assembled state similar to those observed in molecular simulations.

Laowanapiban, P.Kapustina, M.Vonrhein, C.Delarue, M.Koehl, P.Carter, C.W.

(2009) Proc Natl Acad Sci U S A 106: 1790-1795

  • DOI: https://doi.org/10.1073/pnas.0812752106
  • Primary Citation of Related Structures:  
    3FHJ, 3FI0

  • PubMed Abstract: 

    Two new crystal structures of Bacillus stearothermophilus tryptophanyl-tRNA synthetase (TrpRS) afford evidence that a closed interdomain hinge angle requires a covalent bond between AMP and an occupant of either pyrophosphate or tryptophan subsite. They also are within experimental error of a cluster of structures observed in a nonequilibrium molecular dynamics simulation showing partial active-site assembly. Further, the highest energy structure in a minimum action pathway computed by using elastic network models for Open and Pretransition state (PreTS) conformations for the fully liganded TrpRS monomer is intermediate between that simulated structure and a partially disassembled structure from a nonequilibrium molecular dynamics trajectory for the unliganded PreTS. These mutual consistencies provide unexpected validation of inferences drawn from molecular simulations.

  • Organizational Affiliation

    Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC 27599, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Tryptophanyl-tRNA synthetase328Geobacillus stearothermophilusMutation(s): 0 
Gene Names: trpS
Find proteins for P00953 (Geobacillus stearothermophilus)
Explore P00953 
Go to UniProtKB:  P00953
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00953
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on AMP

Download Ideal Coordinates CCD File 
I [auth A]
L [auth D]
O [auth B]
R [auth C]
U [auth E]
I [auth A],
L [auth D],
O [auth B],
R [auth C],
U [auth E],
X [auth F]
C10 H14 N5 O7 P
Query on TRP

Download Ideal Coordinates CCD File 
G [auth A]
J [auth D]
M [auth B]
P [auth C]
S [auth E]
G [auth A],
J [auth D],
M [auth B],
P [auth C],
S [auth E],
V [auth F]
C11 H12 N2 O2
Query on PO4

Download Ideal Coordinates CCD File 
H [auth A]
K [auth D]
N [auth B]
Q [auth C]
T [auth E]
H [auth A],
K [auth D],
N [auth B],
Q [auth C],
T [auth E],
W [auth F]
O4 P
Experimental Data & Validation

Experimental Data

  • Resolution: 2.65 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.210 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 223.606α = 90
b = 91.989β = 134.01
c = 158.322γ = 90
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-02-03
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-11-22
    Changes: Database references
  • Version 1.3: 2020-01-22
    Changes: Database references, Derived calculations
  • Version 1.4: 2023-09-06
    Changes: Data collection, Database references, Derived calculations, Refinement description