6LAY | pdb_00006lay

Domain-swapped dimer structure of a Single-chain Monellin loop1-delta4-QVVAG mutant

• PDB DOI: https://doi.org/10.2210/pdb6LAY/pdb

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


• Deposited: 2019-11-13 Released: 2021-05-19 
• Deposition Author(s): Manjula, R., Subramanian, R., Gosavi, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 
  0.263 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.207 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.210 (Depositor) 

Starting Model: experimental

Literature

Domain-swapped dimer structure of a Single-chain Monellin loop1-delta4-QVVAG mutant

Manjula, R., Subramanian, R., 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: 21.68 kDa 
• Atom Count: 1,514 
• Modeled Residue Count: 184 
• Deposited Residue Count: 186 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Monellin chain B,Monellin chain A	A, B	93	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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free:  0.263 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.207 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.210 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 30.17	α = 90
b = 73.79	β = 100.02
c = 45.99	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-05-19 
Deposition Author(s): Manjula, R., Subramanian, R., Gosavi, S.

Revision History  

• Version 1.0: 2021-05-19
  Type: Initial release
  
• Version 1.1: 2023-11-22
  Changes: Advisory, Data collection, Database references, Refinement description