3FHJ

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.210 

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 U S A 106: 1790-1795

  • DOI: 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 ...

    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
MoleculeChainsSequence LengthOrganismDetailsImage
Tryptophanyl-tRNA synthetase328Geobacillus 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
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
AMP
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]
ADENOSINE MONOPHOSPHATE
C10 H14 N5 O7 P
UDMBCSSLTHHNCD-KQYNXXCUSA-N
 Ligand Interaction
TRP
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]
TRYPTOPHAN
C11 H12 N2 O2
QIVBCDIJIAJPQS-VIFPVBQESA-N
 Ligand Interaction
PO4
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]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • 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
REFMACrefinement
PDB_EXTRACTdata extraction
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing

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