6L4N | pdb_00006l4n

Domain swapped dimer of Monellin loop1 mutant with QVPAG motif

• PDB DOI: https://doi.org/10.2210/pdb6L4N/pdb

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


• Deposited: 2019-10-18 Released: 2021-04-21 
• Deposition Author(s): Manjula, R., Ramaswamy, S., Gosavi, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.43 Å
• R-Value Free: 
  0.253 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.196 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.199 (Depositor) 

Starting Model: experimental

Literature

Domain swapped dimer of Monellin lopp1 mutant with QVPAG motif

Manjula, R., Ramaswamy, S., Gosavi, S.

To be published.

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 PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 21.19 kDa 
• Atom Count: 1,528 
• Modeled Residue Count: 179 
• Deposited Residue Count: 182 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Single chain Monellin	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
MG (Subject of Investigation/LOI)	C [auth A], D [auth A], E [auth A], F [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.43 Å
• R-Value Free:  0.253 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.196 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.199 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.96	α = 90
b = 47.96	β = 90
c = 85.87	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
iMOSFLM	data reduction
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-04-21 
Deposition Author(s): Manjula, R., Ramaswamy, S., Gosavi, S.

Revision History  

• Version 1.0: 2021-04-21
  Type: Initial release
  
• Version 1.1: 2023-11-22
  Changes: Advisory, Data collection, Database references, Refinement description