PDBsum entry 1cxr

Plant protein

PDB id: 1cxr

Contents

Protein chain

46 a.a. *

* Residue conservation analysis

References listed in PDB file

Key reference

Title

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

Authors

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

Ref.

J Magn Reson, 1999, 136, 76-85. [DOI no: 10.1006/jmre.1998.1616]

PubMed id

9887292

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.

Secondary reference #1

Title

Automated assignment of simulated and experimental noesy spectra of proteins by feedback filtering and self-Correcting distance geometry.

Authors

C.Mumenthaler, W.Braun.

Ref.

J Mol Biol, 1995, 254, 465-480. [DOI no: 10.1006/jmbi.1995.0631]

PubMed id

7490763

Figure 5.
Figure 5. (a) Medium range and (b) long range distance constraints derived from the unambiguous assignment list (unambiguous AL) during the different NOAH cycles. The three curves correspond to the data set DEN1 (continuous line), TEN1 (broken line) and REP1 (dotted line).

Figure 9.
Figure 9. Stereoview of the NMR reference structure of dendrotoxin K (Berndt et al., 1993) where the distance constraints derived from all wrong assignments made in the calculation DEN1 are drawn as green and red lines. The green lines are constraints which are fulfilled in the NMR structure, the red lines are those constraints which are violated.

The above figures are reproduced from the cited reference with permission from Elsevier

Secondary reference #2

Title

Automated combined assignment of noesy spectra and three-Dimensional protein structure determination.

Authors

C.Mumenthaler, P.Güntert, W.Braun, K.Wüthrich.

Ref.

J Biomol Nmr, 1997, 10, 351-362.

PubMed id

9460241

Secondary reference #3

Title

Combined automated assignment of nmr spectra and calculation of three- Dimensional protein structures

Authors

Y.Xu, C. H.Schein, W.Braun.

Ref.

biological magnetic, 1999, 17, 37.

Secondary reference #4

Title

A program, Fantom, For energy refinement of polypeptides and proteins using a newton-Raphson minimizer in the torsion angle space

Authors

Th.Schaumann, W.Braun, K.Wuthrich.

Ref.

biopolymers, 1990, 29, 679.

Secondary reference #5

Title

Exact and efficient analytical calculation of the accessible surface areas and their gradients macromolecules

Authors

R.Fraczkiewicz, W.Braun.

Ref.

j comput chem, 1998, 19, 319.