1XXN

Crystal structure of a mesophilic xylanase A from Bacillus subtilis 1A1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.171 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Correlation of temperature induced conformation change with optimum catalytic activity in the recombinant G/11 xylanase A from Bacillus subtilis strain 168 (1A1).

Murakami, M.T.Arni, R.K.Vieira, D.S.Degreve, L.Ruller, R.Ward, R.J.

(2005) Febs Lett. 579: 6505-6510

  • DOI: 10.1016/j.febslet.2005.10.039

  • PubMed Abstract: 
  • The 1.7A resolution crystal structure of recombinant family G/11 beta-1,4-xylanase (rXynA) from Bacillus subtilis 1A1 shows a jellyroll fold in which two curved beta-sheets form the active-site and substrate-binding cleft. The onset of thermal denatu ...

    The 1.7A resolution crystal structure of recombinant family G/11 beta-1,4-xylanase (rXynA) from Bacillus subtilis 1A1 shows a jellyroll fold in which two curved beta-sheets form the active-site and substrate-binding cleft. The onset of thermal denaturation of rXynA occurs at 328 K, in excellent agreement with the optimum catalytic temperature. Molecular dynamics simulations at temperatures of 298-328 K demonstrate that below the optimum temperature the thumb loop and palm domain adopt a closed conformation. However, at 328 K these two domains separate facilitating substrate access to the active-site pocket, thereby accounting for the optimum catalytic temperature of the rXynA.


    Organizational Affiliation

    Department of Physics, IBILCE/UNESP, Cristovão Colombo 2265, São José do Rio Preto, São Paulo, Brazil.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Endo-1,4-beta-xylanase A
A
185Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: xynA
EC: 3.2.1.8
Find proteins for P18429 (Bacillus subtilis (strain 168))
Go to UniProtKB:  P18429
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SRT
Query on SRT

Download SDF File 
Download CCD File 
A
S,R MESO-TARTARIC ACID
C4 H6 O6
FEWJPZIEWOKRBE-XIXRPRMCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.171 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 50.931α = 90.00
b = 70.499β = 90.00
c = 42.044γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
SCALEPACKdata scaling
MAR345data collection
AMoREphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-10-18
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2013-03-06
    Type: Other
  • Version 1.4: 2017-10-11
    Type: Refinement description