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: 2.70 Å
  • R-Value Free: 
    0.220 (Depositor), 0.260 (DCC) 
  • R-Value Work: 
    0.190 (Depositor), 0.250 (DCC) 
  • R-Value Observed: 
    0.190 (Depositor) 

wwPDB Validation   3D Report Full Report


This is version 1.5 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 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.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Tryptophanyl-tRNA synthetase
A, B, C, D, E
326Geobacillus stearothermophilusMutation(s): 0 
Gene Names: TrpS
EC: 6.1.1.2
UniProt
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
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
AMP
Query on AMP

Download Ideal Coordinates CCD File 
AA [auth C]
BB [auth L]
DA [auth D]
EB [auth M]
GA [auth E]
ADENOSINE MONOPHOSPHATE
C10 H14 N5 O7 P
UDMBCSSLTHHNCD-KQYNXXCUSA-N
TRP
Query on TRP

Download Ideal Coordinates CCD File 
BA [auth D]
CB [auth M]
EA [auth E]
FB [auth N]
HA [auth F]
TRYPTOPHAN
C11 H12 N2 O2
QIVBCDIJIAJPQS-VIFPVBQESA-N
PO4
Query on PO4

Download Ideal Coordinates CCD File 
AB [auth L]
CA [auth D]
DB [auth M]
FA [auth E]
GB [auth N]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A, B, C, D, E
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free:  0.220 (Depositor), 0.260 (DCC) 
  • R-Value Work:  0.190 (Depositor), 0.250 (DCC) 
  • R-Value Observed: 0.190 (Depositor) 
Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 122.032α = 79.9
b = 122.396β = 80.52
c = 122.341γ = 79.81
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
SHARPphasing
SOLOMONphasing
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data 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: 2017-11-01
    Changes: Refinement description, Source and taxonomy
  • Version 1.3: 2017-11-22
    Changes: Database references
  • Version 1.4: 2024-03-13
    Changes: Data collection, Database references, Derived calculations, Source and taxonomy, Structure summary
  • Version 1.5: 2024-11-20
    Changes: Structure summary