PDBsum entry: 1nar

Plant seed protein

PDB-id: 1nar

Contents

Description

Header details

Header records

References

PROCHECK

Protein chain

289 a.a. *

Waters ×513

* Residue conservation analysis

Tools

Clefts Calculation

PDB id:

1nar

Name:

Plant seed protein

Title:

Crystal structure of narbonin refined at 1.8 angstroms resolution

Structure:

Narbonin. Chain: a. Engineered: yes

Source:

Vicia narbonensis. Organism_taxid: 3912

UniProt:

Q08884 (Q08884_VICNA)

Seq:

Struc:

Seq:

291 a.a.

Struc:

289 a.a.*

Key:	PfamA domain
Secondary structure	CATH domain

* PDB and UniProt seqs differ at 1 residue position (black cross)

Resolution:

1.80Å

R-factor:

0.159

Authors:

M.Hennig,B.Schlesier,K.S.Wilson

Key ref:

M.Hennig et al. (1995). Crystal structure of narbonin at 1.8 A resolution.. Acta Crystallogr D Biol Crystallogr, 51, 177-189. [PubMed id: 15299319] [DOI: 10.1107/S0907444994009807]

Date:

10-Sep-93

Release date:

31-Jan-94

Quick_links

Procheck

Clefts

Surface

Key reference

DOI no: 10.1107/S0907444994009807

Acta Crystallogr D Biol Crystallogr 51:177-189 (1995)

PubMed id: 15299319

Crystal structure of narbonin at 1.8 A resolution.

M.Hennig, S.Pfeffer-Hennig, Z.Dauter, K.S.Wilson, B.Schlesier, V.H.Nong.

ABSTRACT

The three-dimensional structure of narbonin, a seed protein from Vicia narbonensis L, has been determined at 1.8 A resolution. Phase information was obtained by multiple isomorphous replacement and optimized anomalous dispersion. The narbonin structure was initially traced with only 17% amino-acid sequence information and preliminarily refined to a crystallographic R-factor of 16.5%. It is now refined to 15.9% using full sequence information derived from cDNA and after the addition of more solvent molecules. The monomeric molecule of narbonin is an eight-stranded parallel beta-barrel surrounded by alpha-helices in a beta/alpha-topology similar to that first observed in triose phosphate isomerase. Differences exist in the N-terminal part of the polypeptide chain, where the first helix is replaced by a loop and the second beta-strand is followed by an additional antiparallel alpha-sheet placed parallel on top of alpha-helices alpha3 and alpha4. Two short additional secondary structures are present. The first, an alpha-helix, is situated between the seventh beta-strand and the following helix, and the second, which is a 3(10) helix, between the eighth strand and the C-terminal helix. The most striking observation is the lack of a known enzymatic function for narbonin, because all TIM-like structures known so far are enzymes.

Selected figure(s)

Figure 13.
Fig. 13. Drawings of th C-terminal entrance of the barrel; (a) shows the view along the barrel axis and (b) the side view rotated by 90 °. For clarity, not all the side chains are repeated here (MOLSCRIPT; Kraulis, 1991).

Figure 14.
Fig. 14. Superposition of the C- terminal entrance of the barrel without metal binding in heavy ines and with a mercury ion bound o His l30 in light lines. The dotted shere indicates the position of the mercury ion and * indicates con- srved water molecules.

The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (1995, 51, 177-189) copyright 1995.

Figures were selected by an automated process.