6JBP

Structure of MP-4 from Mucuna pruriens at 2.22 Angstroms


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.22 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.181 

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This is version 1.1 of the entry. See complete history


Literature

The structure of MP-4 from Mucuna pruriens at 2.22 angstrom resolution.

Jain, A.Kumar, A.Shikhi, M.Kumar, A.Nair, D.T.Salunke, D.M.

(2020) Acta Crystallogr F Struct Biol Commun 76: 47-57

  • DOI: 10.1107/S2053230X20000199
  • Primary Citation of Related Structures:  
    6JBP

  • PubMed Abstract: 
  • The structure of the MP-4 protein was previously determined at a resolution of 2.8 Å. Owing to the unavailability of gene-sequence information at the time, the side-chain assignment was carried out on the basis of a partial sequence available through ...

    The structure of the MP-4 protein was previously determined at a resolution of 2.8 Å. Owing to the unavailability of gene-sequence information at the time, the side-chain assignment was carried out on the basis of a partial sequence available through Edman degradation, sequence homology to orthologs and electron density. The structure of MP-4 has now been determined at a higher resolution (2.22 Å) in another space group and all of the structural inferences that were presented in the previous report of the structure were validated. In addition, the present data allowed an improved assignment of side chains and enabled further analysis of the MP-4 structure, and the accuracy of the assignment was confirmed by the recently available gene sequence. The study reinforces the traditional concept that conservative interpretations of relatively low-resolution structures remain correct even with the availability of high-resolution data.


    Related Citations: 
    • MP-4 Contributes to Snake Venom Neutralization by Mucuna pruriens Seeds through an Indirect Antibody-mediated Mechanism.
      Kumar, A., Gupta, C., Nair, D.T., Salunke, D.M.
      (2016) J Biol Chem 291: 11373

    Organizational Affiliation

    International Centre for Genetic Engineering and Biotechnology (ICGEB), Aruna Asaf Ali Marg, New Delhi 110 067, India.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Kunitz-type trypsin inhibitor-like 2 proteinB179Mucuna pruriensMutation(s): 0 
Gene Names: PIP20-2CR513_60827
Find proteins for A0A371E4L6 (Mucuna pruriens)
Explore A0A371E4L6 
Go to UniProtKB:  A0A371E4L6
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.22 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.181 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 75.46α = 90
b = 75.46β = 90
c = 94.23γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2020-01-29
    Type: Initial release
  • Version 1.1: 2020-02-26
    Changes: Database references