8TM8 | pdb_00008tm8

Monomer structure of monellin loop1 mutant (YENKG)

• PDB DOI: https://doi.org/10.2210/pdb8TM8/pdb

• Classification: PLANT PROTEIN
• Organism(s): Dioscoreophyllum cumminsii
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2023-07-28 Released: 2024-12-18 
• Deposition Author(s): Manjula, R., Pavithra, G.C., Ramaswamy, S., Gosavi, S.
• Funding Organization(s): Other private

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.26 Å
• R-Value Free: 
  0.261 (Depositor), 0.262 (DCC) 
• R-Value Work: 
  0.192 (Depositor), 0.195 (DCC) 
• R-Value Observed: 
  0.199 (Depositor) 

Starting Model: experimental

Literature

Monomer structure of monellin loop1 mutant (YENKG)

Pavithra, G.C., Manjula, R., Ramaswamy, S., Gosavi, S.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 21.42 kDa 
• Atom Count: 1,500 
• Modeled Residue Count: 176 
• Deposited Residue Count: 182 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Monellin chain B,Monellin chain A	A, B	91	Dioscoreophyllum cumminsii	Mutation(s): 0
UniProt
Find proteins for P02881 (Dioscoreophyllum cumminsii) Explore P02881  Go to UniProtKB:  P02881
Find proteins for P02882 (Dioscoreophyllum cumminsii) Explore P02882  Go to UniProtKB:  P02882
UniProt Groups	P02881P02882

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NA (Subject of Investigation/LOI)	C [auth B], D [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.26 Å
• R-Value Free:  0.261 (Depositor), 0.262 (DCC) 
• R-Value Work:  0.192 (Depositor), 0.195 (DCC) 
• R-Value Observed: 0.199 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 29.139	α = 90
b = 58.789	β = 91.91
c = 45.21	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-12-18 
Deposition Author(s): Manjula, R., Pavithra, G.C., Ramaswamy, S., Gosavi, S.

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Funding Organization	Location	Grant Number
Other private		--

Revision History  

• Version 1.0: 2024-12-18
  Type: Initial release