1F8Q

CRYSTAL STRUCTURE OF ALPHA-MOMORCHARIN IN ACETONITRILE-WATER MIXTURE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.204 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

Crystal structure of alpha-momorcharin in 80% acetonitrile--water mixture

Zhu, G.Huang, Q.Qian, M.Tang, Y.

(2001) Biochim Biophys Acta 1548: 152-158

  • DOI: 10.1016/s0167-4838(01)00235-7
  • Primary Citation of Related Structures:  
    1F8Q

  • PubMed Abstract: 
  • Crystals of alpha-momorcharin (MMC) were cross-linked and soaked in an 80% acetonitrile--water mixture and X-ray data were collected to 2.2 A resolution. MMC is a ribosome-inactivating protein with a sugar chain on Asn-227. In previous studies, the whole conformation of the sugar chain could not be obtained in the aqueous system ...

    Crystals of alpha-momorcharin (MMC) were cross-linked and soaked in an 80% acetonitrile--water mixture and X-ray data were collected to 2.2 A resolution. MMC is a ribosome-inactivating protein with a sugar chain on Asn-227. In previous studies, the whole conformation of the sugar chain could not be obtained in the aqueous system. Here the structure of MMC in a low water system is shown to be similar to the native one, but the sugar chain on Asn-227 is defined by the electron density map. Several oxygen atoms of the oligosaccharide formed intramolecular hydrogen bonds to the protein moiety. The conformation of the residues in the active center is similar to that in the aqueous system. Our results show conformational alteration of the tetrasaccharide of MMC in organic media. They indicate that the oligosaccharides are more rigid in organic solvents. X-ray determination in organic media may be used to solve some structures of oligosaccharides linked to glycoproteins.


    Related Citations: 
    • Studies on Crystal Structures, Active-Centre Geometry and Depurinating Mechanism of Two Ribosome-Inactivating Proteins
      Huang, Q., Liu, S., Tang, Y., Jin, S., Wang, Y.
      (1995) Biochem J 309: 285

    Organizational Affiliation

    Department of Chemistry, Peking University, Beijing 100871, PR China.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ALPHA-MOMORCHARINA263Momordica charantiaMutation(s): 0 
EC: 3.2.2.22
UniProt
Find proteins for P16094 (Momordica charantia)
Explore P16094 
Go to UniProtKB:  P16094
Protein Feature View
Expand
  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
alpha-D-xylopyranose-(1-2)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseB4N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G19453SD
GlyCosmos:  G19453SD
GlyGen:  G19453SD
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PTD
Query on PTD

Download Ideal Coordinates CCD File 
C [auth A], D [auth A], E [auth A]PENTANEDIAL
C5 H8 O2
SXRSQZLOMIGNAQ-UHFFFAOYSA-N
 Ligand Interaction
CCN
Query on CCN

Download Ideal Coordinates CCD File 
F [auth A], G [auth A]ACETONITRILE
C2 H3 N
WEVYAHXRMPXWCK-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.204 
  • Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 131.51α = 90
b = 131.51β = 90
c = 39.81γ = 120
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
X-PLORphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2000-07-26
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.3: 2017-10-04
    Changes: Refinement description
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Structure summary