PDBsum entry 1ab1

Plant seed protein

PDB id

1ab1

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Contents

			Protein chain

					46 a.a. *

			Ligands

					EOH

* Residue conservation analysis

PDB id:

1ab1

Links

Name:

Plant seed protein

Title:

Si form crambin

Structure:

Crambin (ser22/ile25). Chain: a

Source:

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

Resolution:

0.89Å

R-factor:

0.147

Authors:

M.M.Teeter,A.Yamano

Key ref:

A.Yamano et al. (1997). Crystal structure of Ser-22/Ile-25 form crambin confirms solvent, side chain substate correlations. J Biol Chem, 272, 9597-9600. PubMed id: 9092482

Date:

31-Jan-97

Release date:

12-Aug-97

PROCHECK

	Headers

	References

Protein chain

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

Seq: Struc:					46 a.a. 46 a.a.*

Key:

Secondary structure

CATH domain

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

	J Biol Chem 272:9597-9600 (1997)
PubMed id: 9092482

Crystal structure of Ser-22/Ile-25 form crambin confirms solvent, side chain substate correlations.
A.Yamano, N.H.Heo, M.M.Teeter.

ABSTRACT

It is not agreed that correlated positions of disordered protein side chains (substate correlations) can be deduced from diffraction data. The pure Ser-22/Ile-25 (SI form) crambin crystal structure confirms correlations deduced for the natural, mixed sequence form of crambin crystals. Physical separation of the mixed form into pure SI form and Pro-22/Leu-25 (PL form) crambin and the PL form crystal structure determination (Yamano, A., and Teeter, M. M. (1994) J. Biol. Chem. 269, 13956-13965) support the proposed (Teeter, M. M., Roe, S. M., and Heo, N. H. (1993) J. Mol. Biol. 230, 292-311) correlation model. Electron density of mixed form crambin crystals shows four possible pairs of side chain conformations for heterogeneous residue 22 and nearby Tyr-29 (2(2) = 4, two conformations for each of two side chains). One combination can be eliminated because of short van der Waals' contacts. However, only two alternates have been postulated to exist in mixed form crambin: Pro-22/Tyr-29A and Ser-22/Tyr-29B. In crystals of the PL form, Pro-22 and Tyr-29A are found to be in direct van der Waals' contact (Yamano, A., and Teeter, M. M. (1994) J. Biol. Chem. 269, 13956-13965). Comparison of the SI form structure with the mixed form electron density confirms that the fourth combination of side chains does not occur and that side chain correlations are mediated by water networks.

Literature references that cite this PDB file's key reference

PubMed id

Reference

20823552

F.Pavelcík, and J.Václavík (2010).
Performance of phased rotation, conformation and translation function: accurate protein model building with tripeptidic and tetrapeptidic fragments.

Acta Crystallogr D Biol Crystallogr, 66, 1012-1023.

17139088

U.D.Ramirez, and D.M.Freymann (2006).
Analysis of protein hydration in ultrahigh-resolution structures of the SRP GTPase Ffh.

Acta Crystallogr D Biol Crystallogr, 62, 1520-1534.

PDB codes:

2j45 2j46

15765547

M.Vila-Perelló, and D.Andreu (2005).
Characterization and structural role of disulfide bonds in a highly knotted thionin from Pyrularia pubera.

Biopolymers, 80, 697-707.

16084753

P.B.Pelegrini, and O.L.Franco (2005).
Plant gamma-thionins: novel insights on the mechanism of action of a multi-functional class of defense proteins.

Int J Biochem Cell Biol, 37, 2239-2253.

15613085

B.Stec, O.Markman, U.Rao, G.Heffron, S.Henderson, L.P.Vernon, V.Brumfeld, and M.M.Teeter (2004).
Proposal for molecular mechanism of thionins deduced from physico-chemical studies of plant toxins.

J Pept Res, 64, 210-224.

14739317

M.M.Teeter (2004).
Myoglobin cavities provide interior ligand pathway.

Protein Sci, 13, 313-318.

11572978

M.M.Teeter, A.Yamano, B.Stec, and U.Mohanty (2001).
On the nature of a glassy state of matter in a hydrated protein: Relation to protein function.

Proc Natl Acad Sci U S A, 98, 11242-11247.

PDB codes:

1jxt 1jxu 1jxw 1jxx 1jxy

10737790

C.Jelsch, M.M.Teeter, V.Lamzin, V.Pichon-Pesme, R.H.Blessing, and C.Lecomte (2000).
Accurate protein crystallography at ultra-high resolution: valence electron distribution in crambin.

Proc Natl Acad Sci U S A, 97, 3171-3176.

PDB code:

1ejg

10430894

F.Xu, and T.A.Cross (1999).
Water: foldase activity in catalyzing polypeptide conformational rearrangements.

Proc Natl Acad Sci U S A, 96, 9057-9061.

The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.