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 
  • R-Value Work: 0.190 
  • R-Value Observed: 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 U S A 106: 1790-1795

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

  • 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)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Tryptophanyl-tRNA synthetase
A, B, C, D, E, F, G, H
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
UniProt
Find proteins for P00953 (Geobacillus stearothermophilus)
Explore P00953 
Go to UniProtKB:  P00953
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
AMP (Subject of Investigation/LOI)
Query on AMP

Download Ideal Coordinates CCD File 
AA [auth C] , BB [auth L] , DA [auth D] , EB [auth M] , GA [auth E] , HB [auth N] , JA [auth F] , KB [auth O] , 
AA [auth C],  BB [auth L],  DA [auth D],  EB [auth M],  GA [auth E],  HB [auth N],  JA [auth F],  KB [auth O],  MA [auth G],  NB [auth P],  PA [auth H],  QB [auth Q],  SA [auth I],  TB [auth R],  U [auth A],  VA [auth J],  X [auth B],  YA [auth K]
ADENOSINE MONOPHOSPHATE
C10 H14 N5 O7 P
UDMBCSSLTHHNCD-KQYNXXCUSA-N
 Ligand Interaction
TRP (Subject of Investigation/LOI)
Query on TRP

Download Ideal Coordinates CCD File 
BA [auth D] , CB [auth M] , EA [auth E] , FB [auth N] , HA [auth F] , IB [auth O] , KA [auth G] , LB [auth P] , 
BA [auth D],  CB [auth M],  EA [auth E],  FB [auth N],  HA [auth F],  IB [auth O],  KA [auth G],  LB [auth P],  NA [auth H],  OB [auth Q],  QA [auth I],  RB [auth R],  S [auth A],  TA [auth J],  V [auth B],  WA [auth K],  Y [auth C],  ZA [auth L]
TRYPTOPHAN
C11 H12 N2 O2
QIVBCDIJIAJPQS-VIFPVBQESA-N
 Ligand Interaction
PO4
Query on PO4

Download Ideal Coordinates CCD File 
AB [auth L] , CA [auth D] , DB [auth M] , FA [auth E] , GB [auth N] , IA [auth F] , JB [auth O] , LA [auth G] , 
AB [auth L],  CA [auth D],  DB [auth M],  FA [auth E],  GB [auth N],  IA [auth F],  JB [auth O],  LA [auth G],  MB [auth P],  OA [auth H],  PB [auth Q],  RA [auth I],  SB [auth R],  T [auth A],  UA [auth J],  W [auth B],  XA [auth K],  Z [auth C]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A , B , C , D , E , F , G , H , 
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: 2.70 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.190 
  • 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