4ATL

Crystal structure of Raucaffricine glucosidase in complex with Glucose


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.52 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.174 

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Ligand Structure Quality Assessment 


This is version 1.3 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:  
    4ATD, 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 participates in alkaloid biosynthesis in the plant Rauvolfia ...

    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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
RAUCAFFRICINE-O-BETA-D-GLUCOSIDASEA, B513Rauvolfia serpentinaMutation(s): 0 
Gene Names: RGVGT
EC: 3.2.1.125 (PDB Primary Data), 2.4.1.219 (UniProt)
UniProt
Find proteins for Q9SPP9 (Rauvolfia serpentina)
Explore Q9SPP9 
Go to UniProtKB:  Q9SPP9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9SPP9
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BGC
Query on BGC

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
beta-D-glucopyranose
C6 H12 O6
WQZGKKKJIJFFOK-VFUOTHLCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.52 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.174 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 102.774α = 90
b = 127.329β = 90
c = 215.837γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
Auto-Rickshawphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-01-30
    Type: Initial release
  • Version 1.1: 2013-08-07
    Changes: Database references
  • Version 1.2: 2019-07-17
    Changes: Data collection
  • Version 1.3: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Other, Structure summary