4ATD

Crystal structure of native Raucaffricine glucosidase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.175 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

High Speed X-Ray Analysis of Plant Enzymes at Room Temperature

Xia, L.Rajendran, C.Ruppert, M.Panjikar, S.Wang, M.Stoeckigt, J.

(2013) Phytochemistry 91: 88

  • DOI: 10.1016/j.phytochem.2012.05.009
  • Primary Citation of Related Structures:  4ATL, 4EK7

  • PubMed Abstract: 
  • X-ray measurements at room temperature (295 K) deliver high quality data sets with unprecedented speed (<2 min), as shown for crystallized raucaffricine-O-β-D-glucosidase (RG), its mutant RG-Glu186Gln and several ligand complexes of the enzyme which ...

    X-ray measurements at room temperature (295 K) deliver high quality data sets with unprecedented speed (<2 min), as shown for crystallized raucaffricine-O-β-D-glucosidase (RG), its mutant RG-Glu186Gln and several ligand complexes of the enzyme which participates in alkaloid biosynthesis in the plant Rauvolfia. The data obtained are compared with data sets measured under typical cryo conditions (100K). Under both conditions, density maps are highly comparable and favor the described protocol for room temperature measurements, potentially paving the way for future crystallographic studies capturing biosynthetic pathway intermediates.


    Related Citations: 
    • Structures of Alkaloid Biosynthetic Glucosidases Decode Substrate Specificity.
      Xia, L.,Ruppert, M.,Wang, M.,Panjikar, S.,Lin, H.,Rajendran, C.,Barleben, L.,Stockigt, J.
      (2012) Acs Chem.Biol. 7: 226


    Organizational Affiliation

    Institute of Materia Medica, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, PR China.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
RAUCAFFRICINE-O-BETA-D-GLUCOSIDASE
A, B
513Rauvolfia serpentinaGene Names: RG (VGT)
EC: 3.2.1.125, 2.4.1.219
Find proteins for Q9SPP9 (Rauvolfia serpentina)
Go to UniProtKB:  Q9SPP9
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.175 
  • Space Group: I 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 102.237α = 90.00
b = 127.253β = 90.00
c = 216.111γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
Auto-Rickshawphasing
XDSdata reduction
XSCALEdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-01-16
    Type: Initial release
  • Version 1.1: 2013-06-19
    Type: Database references