PDBsum entry 1cxr

Plant protein

PDB id: 1cxr

Contents

Protein chain

46 a.a. *

* Residue conservation analysis

PDB id:

1cxr

Name:

Plant protein

Title:

Automated 2d noesy assignment and structure calculation of crambin(s22/i25) with self-correcting distance geometry based noah/diamod programs

Structure:

Crambin. Chain: a. Fragment: isoform of crambin (46 residues). Mutation: yes

Source:

Crambe hispanica subsp. Abyssinica. Organism_taxid: 3721. Strain: subsp. Abyssinica. Organ: seed

NMR struc:

10 models

Authors:

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

Key ref:

Y.Xu et al. (1999). 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. PubMed id: 9887292 DOI: 10.1006/jmre.1998.1616

Date:

30-Aug-99 Release date: 07-Sep-99

Protein chain

P01542  (CRAM_CRAAB) -  Crambin from Crambe hispanica subsp. abyssinica

Seq: 46 a.a.

Struc: 46 a.a.*

* PDB and UniProt seqs differ at 2 residue positions (black crosses)

DOI no: 10.1006/jmre.1998.1616

J Magn Reson 136:76-85 (1999)

PubMed id: 9887292

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

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

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.