1CXR

AUTOMATED 2D NOESY ASSIGNMENT AND STRUCTURE CALCULATION OF CRAMBIN(S22/I25) WITH SELF-CORRECTING DISTANCE GEOMETRY BASED NOAH/DIAMOD PROGRAMS


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 40 
  • Conformers Submitted: 10 
  • Selection Criteria: STRUCTURES WITH THE LEAST RESTRAINT VIOLATIONS,STRUCTURES WITH THE LOWEST ENERGY,TARGET FUNCTION 

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This is version 1.5 of the entry. See complete history


Literature

Automated 2D NOESY assignment and structure calculation of Crambin(S22/I25) with the self-correcting distance geometry based NOAH/DIAMOD programs.

Xu, Y.Wu, J.Gorenstein, D.Braun, W.

(1999) J Magn Reson (1969 136: 76-85

  • DOI: https://doi.org/10.1006/jmre.1998.1616
  • Primary Citation of Related Structures:  
    1CXR

  • PubMed Abstract: 

    The NOAH/DIAMOD program suite was used to automatically assign an experimental 2D NOESY spectrum of the 46 residue protein crambin(S22/I25), using feedback filtering and self-correcting distance geometry (SECODG). Automatically picked NOESY cross peaks were combined with 157 manually assigned peaks to start NOAH/DIAMOD calculations. At each cycle, DIAMOD was used to calculate an ensemble of 40 structures from these NOE distance constraints and random starting structures. The 10 structures with smallest target function values were analyzed by the structure-based filter, NOAH, and a new set of possible assignments was automatically generated based on chemical shifts and distance constraints violations. After 60 iterations and final energy minimization, the 10 structures with smallest target functions converged to 1.48 A for backbone atoms. Despite several missing chemical shifts, 426 of 613 NOE peaks were unambiguously assigned; 59 peaks were ambiguously assigned. The remaining 128 peaks picked automatically by FELIX are probably primarily noise peaks, with a few real peaks that were not assigned by NOAH due to the incomplete proton chemical shifts list.


  • Organizational Affiliation

    Sealy Center for Structural Biology and Department of Human Biological Chemistry and Genetics, University of Texas Medical Branch, Galveston, Texas, 77555-1157, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
CRAMBIN46Crambe hispanica subsp. abyssinicaMutation(s): 1 
UniProt
Find proteins for P01542 (Crambe hispanica subsp. abyssinica)
Explore P01542 
Go to UniProtKB:  P01542
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP01542
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 40 
  • Conformers Submitted: 10 
  • Selection Criteria: STRUCTURES WITH THE LEAST RESTRAINT VIOLATIONS,STRUCTURES WITH THE LOWEST ENERGY,TARGET FUNCTION 

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1999-09-07
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2018-01-24
    Changes: Database references, Derived calculations
  • Version 1.4: 2018-03-14
    Changes: Database references
  • Version 1.5: 2024-11-20
    Changes: Data collection, Database references, Structure summary