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 

wwPDB Validation 3D Report Full Report


This is version 1.4 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. 136: 76-85

  • DOI: 10.1006/jmre.1998.1616

  • 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 pea ...

    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.


    Related Citations: 
    • Automated Assignment of Simulated, Experimental Noesy Spectra of Proteins by Feedback Filtering and Self-Correcting Distance Geometry
      Mumenthaler, C.,Braun, W.
      (1995) J.Mol.Biol. 254: 465
    • Exact and Efficient Analytical Calculation of the Accessible Surface Areas and Their Gradients Macromolecules
      Fraczkiewicz, R.,Braun, W.
      (1998) J.Comput.Chem. 19: 319
    • Automated Combined Assignment of Noesy Spectra and Three-Dimensional Protein Structure Determination
      Mumenthaler, C.,Guntert, P.,Braun, W.,Wuthrich, K.
      (1997) J.Biomol.NMR 10: 351
    • A Program, Fantom, for Energy Refinement of Polypeptides and Proteins Using a Newton-Raphson Minimizer in the Torsion Angle Space
      Schaumann, T.H.,Braun, W.,Wuthrich, K.
      (1990) Biopolymers 29: 679
    • Combined Automated Assignment of NMR Spectra and Calculation of Three- Dimensional Protein Structures
      Xu, Y.,Schein, C.H.,Braun, W.
      (1999) Biological Magnetic Resonance 17: 37


    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CRAMBIN
A
46Crambe hispanica subsp. abyssinicaMutations: P22S
Gene Names: THI2
Find proteins for P01542 (Crambe hispanica subsp. abyssinica)
Go to UniProtKB:  P01542
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 
  • Olderado: 1CXR Olderado

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1999-09-07
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2018-01-24
    Type: Database references, Derived calculations
  • Version 1.4: 2018-03-14
    Type: Database references