1CF5

BETA-MOMORCHARIN STRUCTURE AT 2.55 A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.172 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Three-dimensional structure of beta-momorcharin at 2.55 A resolution.

Yuan, Y.R.He, Y.N.Xiong, J.P.Xia, Z.X.

(1999) Acta Crystallogr.,Sect.D 55: 1144-1151


  • PubMed Abstract: 
  • Beta-Momorcharin (Mr approximately 29 kDa) is a single-chained ribosome-inactivating protein (RIP) with a branched hexasaccharide bound to Asn51. The crystal structure of beta-momorcharin has been determined using the molecular-replacement method and ...

    Beta-Momorcharin (Mr approximately 29 kDa) is a single-chained ribosome-inactivating protein (RIP) with a branched hexasaccharide bound to Asn51. The crystal structure of beta-momorcharin has been determined using the molecular-replacement method and refined to 2. 55 A resolution. The final structural model gave an R factor of 17. 2% and root-mean-square deviations of 0.016 A and 1.76 degrees from ideal bond lengths and bond angles, respectively. beta-Momorcharin contains nine alpha-helices, two 310 helices and three beta-sheets, and its overall structure is similar to those of other single-chained RIPs. Residues Tyr70, Tyr109, Glu158 and Arg161 are expected to define the active site of beta-momorcharin as an rRNA N-glycosidase. The oligosaccharide is linked to the protein through an N-glycosidic bond, beta-GlcNAc-(1-N)-Asn51, and stretches from the surface of the N-terminal domain far from the active site, which suggests that it should not play a role in enzymatic function. The oligosaccharide of each beta-momorcharin molecule interacts with the protein through hydrogen bonds, although in the crystals most of these are intermolecular interactions with the protein atoms in an adjacent unit cell. This is the first example of an RIP structure which provides information about the three-dimensional structure and binding site of the oligosaccharide in the active chains of RIPs.


    Related Citations: 
    • The Determination and Refinement of Three-Dimensional Structure of Beta- Momorcharin at 2.4 A Resolution
      Yuan, Y.-R.,Xiong, J.-P.,Xia, Z.-X.
      (1995) Chin.Chem.Lett. 6: 1053
    • Crystallization and Preliminary Crystallographic Study of Beta-Momorcharin
      Xiong, J.-P.,Xia, Z.-X.,Zhang, L.,Ye, G.-J.,Jin, S.-W.,Wang, Y.
      (1994) J.Mol.Biol. 238: 284


    Organizational Affiliation

    Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 200032, China.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PROTEIN (BETA-MOMORCHARIN)
A, B
249Momordica charantiaGene Names: MAP30 (RIP)
EC: 3.2.2.22
Find proteins for P24817 (Momordica charantia)
Go to UniProtKB:  P24817
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MAN
Query on MAN

Download SDF File 
Download CCD File 
A, B
ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
FUC
Query on FUC

Download SDF File 
Download CCD File 
A, B
ALPHA-L-FUCOSE
C6 H12 O5
SHZGCJCMOBCMKK-SXUWKVJYSA-N
 Ligand Interaction
BMA
Query on BMA

Download SDF File 
Download CCD File 
A, B
BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
A, B
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
XYP
Query on XYP

Download SDF File 
Download CCD File 
A, B
BETA-D-XYLOPYRANOSE
C5 H10 O5
SRBFZHDQGSBBOR-KKQCNMDGSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.172 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 49.090α = 72.98
b = 50.580β = 78.39
c = 61.120γ = 76.97
Software Package:
Software NamePurpose
X-GENdata scaling
MERLOTphasing
X-GENdata reduction
X-PLORrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1999-06-07
    Type: Initial release
  • Version 1.1: 2007-10-16
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Non-polymer description, Version format compliance
  • Version 1.3: 2017-10-04
    Type: Refinement description