3MF9

Computationally designed endo-1,4-beta-xylanase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.172 
  • R-Value Work: 0.128 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Computational design of an endo-1,4-{beta}-xylanase ligand binding site.

Morin, A.Kaufmann, K.W.Fortenberry, C.Harp, J.M.Mizoue, L.S.Meiler, J.

(2011) Protein Eng.Des.Sel. 24: 503-516

  • DOI: 10.1093/protein/gzr006
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The field of computational protein design has experienced important recent success. However, the de novo computational design of high-affinity protein-ligand interfaces is still largely an open challenge. Using the Rosetta program, we attempted the i ...

    The field of computational protein design has experienced important recent success. However, the de novo computational design of high-affinity protein-ligand interfaces is still largely an open challenge. Using the Rosetta program, we attempted the in silico design of a high-affinity protein interface to a small peptide ligand. We chose the thermophilic endo-1,4-β-xylanase from Nonomuraea flexuosa as the protein scaffold on which to perform our designs. Over the course of the study, 12 proteins derived from this scaffold were produced and assayed for binding to the target ligand. Unfortunately, none of the designed proteins displayed evidence of high-affinity binding. Structural characterization of four designed proteins revealed that although the predicted structure of the protein model was highly accurate, this structural accuracy did not translate into accurate prediction of binding affinity. Crystallographic analyses indicate that the lack of binding affinity is possibly due to unaccounted for protein dynamics in the 'thumb' region of our design scaffold intrinsic to the family 11 β-xylanase fold. Further computational analysis revealed two specific, single amino acid substitutions responsible for an observed change in backbone conformation, and decreased dynamic stability of the catalytic cleft. These findings offer new insight into the dynamic and structural determinants of the β-xylanase proteins.


    Organizational Affiliation

    Department of Chemistry, Vanderbilt University, Nashville, TN 37235, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Endo-1,4-beta-xylanase
A
193Thermopolyspora flexuosaMutation(s): 6 
Gene Names: xyn11A
EC: 3.2.1.8
Find proteins for Q8GMV7 (Thermopolyspora flexuosa)
Go to UniProtKB:  Q8GMV7
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.172 
  • R-Value Work: 0.128 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 63.778α = 90.00
b = 63.778β = 90.00
c = 106.234γ = 120.00
Software Package:
Software NamePurpose
MOLREPphasing
PROTEUM PLUSdata collection
REFMACrefinement
PROTEUM PLUSdata scaling
PROTEUM PLUSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2010-04-01 
  • Released Date: 2010-11-10 
  • Deposition Author(s): Morin, A., Harp, J.M.

Revision History 

  • Version 1.0: 2010-11-10
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance