3B5L

Crystal Structure of a Novel Engineered Retroaldolase: RA-61


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.203 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

De novo computational design of retro-aldol enzymes.

Jiang, L.Althoff, E.A.Clemente, F.R.Doyle, L.Rothlisberger, D.Zanghellini, A.Gallaher, J.L.Betker, J.L.Tanaka, F.Barbas, C.F.Hilvert, D.Houk, K.N.Stoddard, B.L.Baker, D.

(2008) Science 319: 1387-1391

  • DOI: 10.1126/science.1152692
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The creation of enzymes capable of catalyzing any desired chemical reaction is a grand challenge for computational protein design. Using new algorithms that rely on hashing techniques to construct active sites for multistep reactions, we designed ret ...

    The creation of enzymes capable of catalyzing any desired chemical reaction is a grand challenge for computational protein design. Using new algorithms that rely on hashing techniques to construct active sites for multistep reactions, we designed retro-aldolases that use four different catalytic motifs to catalyze the breaking of a carbon-carbon bond in a nonnatural substrate. Of the 72 designs that were experimentally characterized, 32, spanning a range of protein folds, had detectable retro-aldolase activity. Designs that used an explicit water molecule to mediate proton shuffling were significantly more successful, with rate accelerations of up to four orders of magnitude and multiple turnovers, than those involving charged side-chain networks. The atomic accuracy of the design process was confirmed by the x-ray crystal structure of active designs embedded in two protein scaffolds, both of which were nearly superimposable on the design model.


    Organizational Affiliation

    Department of Biochemistry, University of Washington, Seattle, WA 98195, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Endoxylanase
B
198Thermopolyspora flexuosaMutation(s): 0 
Gene Names: xyn11A
EC: 3.2.1.8
Find proteins for Q8GMV7 (Thermopolyspora flexuosa)
Go to UniProtKB:  Q8GMV7
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
NH4
Query on NH4

Download SDF File 
Download CCD File 
B
AMMONIUM ION
H4 N
QGZKDVFQNNGYKY-UHFFFAOYSA-O
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.203 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 39.190α = 90.00
b = 66.060β = 90.00
c = 66.070γ = 90.00
Software Package:
Software NamePurpose
CrystalCleardata collection
REFMACrefinement
PHASERphasing
d*TREKdata scaling
PDB_EXTRACTdata extraction
CrystalCleardata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-01-22
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Version format compliance