1KRL

Crystal Structure of Racemic DL-monellin in P-1

• PDB DOI: https://doi.org/10.2210/pdb1KRL/pdb

• Classification: PLANT PROTEIN
• Organism(s): Dioscoreophyllum cumminsii
• Mutation(s): No 


• Deposited: 2002-01-10 Released: 2002-02-27 
• Deposition Author(s): Hung, L.W., Kohmura, M., Ariyoshi, Y., Kim, S.H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.293 
• R-Value Work: 0.249 

Literature

Structural differences in D and L-monellin in the crystals of racemic mixture.

Hung, L.W., Kohmura, M., Ariyoshi, Y., Kim, S.H.

(1999) J Mol Biol 285: 311-321

• PubMed: 9878408 
• DOI: https://doi.org/10.1006/jmbi.1998.2308
• Primary Citation of Related Structures:  
  1KRL


• PubMed Abstract: 
  

  The racemic mixture of synthetic d and l-monellin has been crystallized, and its structure has been determined by X-ray crystallography at 1.9 A resolution. The crystal structure consists of two d and two l-monellin molecules in the P1 unit cell with a pseudo-centrosymmetrical arrangement. The final structure reveals small but significant structural differences between d and l-monellin in the same crystal. Possible reasons for these differences and their implications are discussed.

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Organizational Affiliation: 

Department of Chemistry, University of California, Berkeley, CA, 94720, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 22.2 kDa 
• Atom Count: 1,767 
• Modelled Residue Count: 184 
• Deposited Residue Count: 188 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MONELLIN, CHAIN A	A, C	44	Dioscoreophyllum cumminsii	Mutation(s): 0
UniProt
Find proteins for P02881 (Dioscoreophyllum cumminsii) Explore P02881  Go to UniProtKB:  P02881

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
MONELLIN, CHAIN B	B, D	50	Dioscoreophyllum cumminsii	Mutation(s): 0
UniProt
Find proteins for P02882 (Dioscoreophyllum cumminsii) Explore P02882  Go to UniProtKB:  P02882

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.293 
• R-Value Work: 0.249 
• Space Group: P -1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 38.71	α = 90.55
b = 49.07	β = 94.33
c = 53.12	γ = 90.31

Software Package:

Software Name	Purpose
AMoRE	phasing
X-PLOR	refinement
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2002-02-27 
Deposition Author(s): Hung, L.W., Kohmura, M., Ariyoshi, Y., Kim, S.H.

Revision History  

• Version 1.0: 2002-02-27
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2012-03-28
  Changes: Other
• Version 1.4: 2017-10-11
  Changes: Refinement description
• Version 1.5: 2018-01-31
  Changes: Experimental preparation
• Version 1.6: 2024-02-14
  Changes: Data collection, Database references
• Version 1.7: 2024-04-03
  Changes: Refinement description