3FI0

Crystal Structure Analysis of B. stearothermophilus Tryptophanyl-tRNA Synthetase Complexed with Tryptophan, AMP, and Inorganic Phosphate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.190 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

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.Usa 106: 1790-1795

  • DOI: 10.1073/pnas.0812752106
  • Primary Citation of Related Structures:  

  • 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. T ...

    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.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Tryptophanyl-tRNA synthetase
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R
326Geobacillus stearothermophilusMutation(s): 0 
Gene Names: trpS
EC: 6.1.1.2
Find proteins for P00953 (Geobacillus stearothermophilus)
Go to UniProtKB:  P00953
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
TRP
Query on TRP

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R
TRYPTOPHAN
C11 H12 N2 O2
QIVBCDIJIAJPQS-VIFPVBQESA-N
 Ligand Interaction
AMP
Query on AMP

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R
ADENOSINE MONOPHOSPHATE
C10 H14 N5 O7 P
UDMBCSSLTHHNCD-KQYNXXCUSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.190 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 122.032α = 79.90
b = 122.396β = 80.52
c = 122.341γ = 79.81
Software Package:
Software NamePurpose
SOLOMONphasing
HKL-2000data scaling
DENZOdata reduction
HKL-2000data reduction
SHARPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
PHASERphasing
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-02-03
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2017-11-01
    Type: Refinement description, Source and taxonomy
  • Version 1.3: 2017-11-22
    Type: Database references