4ATD | pdb_00004atd

Crystal structure of native Raucaffricine glucosidase

• PDB DOI: https://doi.org/10.2210/pdb4ATD/pdb

• Classification: HYDROLASE
• Organism(s): Rauvolfia serpentina
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2012-05-05 Released: 2013-01-16 
• Deposition Author(s): Xia, L., Rajendran, C., Ruppert, M., Panjikar, S., Wang, M., Stoeckigt, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.206 (Depositor), 0.207 (DCC) 
• R-Value Work: 
  0.175 (Depositor) 
• R-Value Observed: 
  0.175 (Depositor) 

Starting Model: experimental

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

• PubMed: 22704651 
• DOI: https://doi.org/10.1016/j.phytochem.2012.05.009
• Primary Citation 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. 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.

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Organizational Affiliation: 
• Institute of Materia Medica, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, PR China.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PQS (software)

Macromolecule Content 

• Total Structure Weight: 116.14 kDa 
• Atom Count: 8,111 
• Modeled Residue Count: 938 
• Deposited Residue Count: 1,026 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RAUCAFFRICINE-O-BETA-D-GLUCOSIDASE	A, B	513	Rauvolfia serpentina	Mutation(s): 0  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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth A], D [auth A], E [auth A], F [auth B], G [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.206 (Depositor), 0.207 (DCC) 
• R-Value Work:  0.175 (Depositor) 
• R-Value Observed: 0.175 (Depositor) 

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 102.237	α = 90
b = 127.253	β = 90
c = 216.111	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
Auto-Rickshaw	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-01-16 
Deposition Author(s): Xia, L., Rajendran, C., Ruppert, M., Panjikar, S., Wang, M., Stoeckigt, J.

Revision History  

• Version 1.0: 2013-01-16
  Type: Initial release
  
• Version 1.1: 2013-06-19
  Changes: Database references
• Version 1.2: 2019-07-17
  Changes: Data collection, Derived calculations
• Version 1.3: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description