1CXR

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

Summary for 1CXR

• Entry DOI: 10.2210/pdb1cxr/pdb
• Related: 1CCM
• NMR Information: BMRB: 4509
• Descriptor: CRAMBIN (1 entity in total)
• Functional Keywords: crambin, crambe abyssinica, plant seed protein feb. 20, 1997, plant protein
• Biological source: Crambe hispanica subsp. abyssinica
• Cellular location: Secreted: P01542
• Total number of polymer chains: 1
• Total formula weight: 4728.41

Authors

Xu, Y.,Wu, J.,Gorenstein, D.,Braun, W. (deposition date: 1999-08-30, release date: 1999-09-07, Last modification date: 2018-03-14)

Primary citation

Xu, Y.,Wu, J.,Gorenstein, D.,Braun, W.
Automated 2D NOESY assignment and structure calculation of Crambin(S22/I25) with the self-correcting distance geometry based NOAH/DIAMOD programs.
J.Magn.Reson., 136:76-85, 1999

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.

PubMed: 9887292
DOI: 10.1006/jmre.1998.1616

Experimental method

SOLUTION NMR