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TRAP4 (engineered TRAP)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.191 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Rounding up: Engineering 12-Membered Rings from the Cyclic 11-Mer TRAP

Heddle, J.G.Yokoyama, T.Yamashita, I.Park, S.Y.Tame, J.R.H.

(2006) Structure 14: 925-933

  • DOI: 10.1016/j.str.2006.03.013
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The protein TRAP (trp RNA binding attenuation protein) forms a highly thermostable ring-shaped 11-mer. By linking in tandem two, three, or four DNA sequences encoding TRAP monomers, we have engineered new rings that consist of 12 TRAP subunits and bi ...

    The protein TRAP (trp RNA binding attenuation protein) forms a highly thermostable ring-shaped 11-mer. By linking in tandem two, three, or four DNA sequences encoding TRAP monomers, we have engineered new rings that consist of 12 TRAP subunits and bind 12 ligand molecules. The hydrogen bonding pattern and buried surface area within and between subunits are essentially identical between the 11-mer and 12-mer crystal structures. Why do the artificial proteins choose to make single 12-mer rings? The 12-mer rings are highly sterically strained by their peptide linkers and far from thermostable. That proteins choose to adopt a strained conformation of few subunits rather than an unstrained one with 11 subunits demonstrates the importance of entropic factors in controlling protein-protein interactions in general.


    Organizational Affiliation

    Protein Design Laboratory, Yokohama City University, Tsurumi, Suehiro 1-7-29, Yokohama 230-0045, Japan. jgh4@tsurumi.yokohama-cu.ac.jp




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Transcription attenuation protein mtrB
A, B, C
77Geobacillus stearothermophilusMutation(s): 0 
Gene Names: mtrB
Find proteins for Q9X6J6 (Geobacillus stearothermophilus)
Go to UniProtKB:  Q9X6J6
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
TRP
Query on TRP

Download SDF File 
Download CCD File 
B
TRYPTOPHAN
C11 H12 N2 O2
QIVBCDIJIAJPQS-VIFPVBQESA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.191 
  • Space Group: P 4 21 2
Unit Cell:
Length (Å)Angle (°)
a = 109.789α = 90.00
b = 109.789β = 90.00
c = 36.871γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-08-01
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance