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 

Starting Model: experimental
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This is version 1.2 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: https://doi.org/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 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.


  • Organizational Affiliation

    Regional Centre for Biotechnology, NCR Biotech Science Cluster, 3rd Milestone, Faridabad-Gurgaon Expressway, Faridabad 121 001, India.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Kunitz-type trypsin inhibitor-like 2 proteinA [auth B]179Mucuna pruriensMutation(s): 0 
UniProt
Find proteins for A0A371E4L6 (Mucuna pruriens)
Explore A0A371E4L6 
Go to UniProtKB:  A0A371E4L6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A371E4L6
Sequence Annotations
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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  (Full details and data files)

  • Version 1.0: 2020-01-29
    Type: Initial release
  • Version 1.1: 2020-02-26
    Changes: Database references
  • Version 1.2: 2023-11-22
    Changes: Data collection, Database references, Refinement description