Skip to main content
OSTI.GOVU.S. Department of Energy Office of Scientific and Technical Information
U.S. Department of Energy
Office of Scientific and Technical Information
 

ANS complex of St John's wort PR-10 protein with 28 copies in the asymmetric unit: A fiendish combination of pseudosymmetry with tetartohedral twinning

Journal Article · · Acta Crystallographica. Section D: Biological Crystallography (Online)
 [1];  [2];  [3];  [4];  [4];  [5]
  1. Polish Academy of Sciences, Poznan (Poland). Center for Biocrystallogrphic Research.
  2. Argonne National Lab., Argonne, IL (United States). Synchrotron Radiation Research Section.
  3. Poznan Univ. of Medical Sciecnes, Poznan (Poland). Dept. of Organic Chemistry.
  4. Univ. of Cambridge, Cambridge (England). Dept. of Haematology.
  5. Polish Academy of Sciences, Poznan (Poland). Center for Biocrystallogrphic Research; A. Mickiewicz Univ., Poznan (Poland). Dept. of Crystallography.
+ Show Author Affiliations

Hyp-1, a pathogenesis-related class 10 (PR-10) protein from St John's wort (Hypericum perforatum), was crystallized in complex with the fluorescent probe 8-anilino-1-naphthalene sulfonate (ANS). The highly pseudosymmetric crystal has 28 unique protein molecules arranged in columns with sevenfold translational noncrystallographic symmetry (tNCS) along c and modulated X-ray diffraction with intensity crests at l = 7n and l = 7n ± 3. The translational NCS is combined with pseudotetragonal rotational NCS. The crystal was a perfect tetartohedral twin, although detection of twinning was severely hindered by the pseudosymmetry. The structure determined at 2.4 Å resolution reveals that the Hyp-1 molecules (packed as β-sheet dimers) have three novel ligand-binding sites (two internal and one in a surface pocket), which was confirmed by solution studies. In addition to 60 Hyp-1-docked ligands, there are 29 interstitial ANS molecules distributed in a pattern that violates the arrangement of the protein molecules and is likely to be the generator of the structural modulation. In particular, whenever the stacked Hyp-1 molecules are found closer together there is an ANS molecule bridging them.

Research Organization:
Argonne National Laboratory (ANL), Argonne, IL (United States)
Sponsoring Organization:
USDOE
Grant/Contract Number:
AC02-06CH11357
OSTI ID:
1212889
Alternate ID(s):
OSTI ID: 22347699
Journal Information:
Acta Crystallographica. Section D: Biological Crystallography (Online), Journal Name: Acta Crystallographica. Section D: Biological Crystallography (Online) Journal Issue: 4 Vol. 71; ISSN 1399-0047; ISSN ABCRE6
Publisher:
International Union of CrystallographyCopyright Statement
Country of Publication:
United States
Language:
English

References (41)

Stress-induced expression and structure of the putative gene hyp-1 for hypericin biosynthesis journal March 2013
A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding journal May 1976
1-Anilino-8-Naphthalene Sulfonate Anion-Protein Binding Depends Primarily on Ion Pair Formation journal January 1998
Crystal Structures of Two Homologous Pathogenesis-related Proteins from Yellow Lupine journal June 2002
Crystal Structure of a Hypoallergenic Isoform of the Major Birch Pollen Allergen Bet v 1 and its Likely Biological Function as a Plant Steroid Carrier journal January 2003
ANS fluorescence: Potential to augment the identification of the external binding sites of proteins journal March 2007
Lupinus luteus Pathogenesis-Related Protein as a Reservoir for Cytokinin journal May 2008
Crystallographically Mapped Ligand Binding Differs in High and Low IgE Binding Isoforms of Birch Pollen Allergen Bet v 1 journal September 2012
Crystal structure of Hyp-1, a St. John’s wort protein implicated in the biosynthesis of hypericin journal February 2010
Plant pathogenesis-related (PR) proteins: A focus on PR peptides journal November 2008
Signal advance for abscisic acid journal December 2009
Improved R-factors for diffraction data analysis in macromolecular crystallography journal April 1997
X-ray and NMR structure of Bet v 1, the origin of birch pollen allergy journal December 1996
Molecular and Biochemical Characterization of an Enzyme Responsible for the Formation of Hypericin in St. John's Wort ( Hypericum perforatum L.) journal June 2003
Crystal Structure of Vigna radiata Cytokinin-Specific Binding Protein in Complex with Zeatin journal September 2006
Phaser crystallographic software journal July 2007
Automatic multiple-zone rigid-body refinement with a large convergence radius journal July 2009
How to read (and understand) Volume A of International Tables for Crystallography : an introduction for nonspecialists journal August 2010
PROCHECK: a program to check the stereochemical quality of protein structures journal April 1993
ALIGN : a program to superimpose protein coordinates, accounting for insertions and deletions journal December 1997
A short history of SHELX journal December 2007
Accurate bond and angle parameters for X-ray protein structure refinement journal July 1991
The Cambridge Structural Database: a quarter of a million crystal structures and rising journal May 2002
A non-mathematical introduction to the superspace description of modulated structures journal May 2009
Largest likely values for the reliability index journal September 1950
Fluorescent probe conformations: the crystal and molecular structure of hexaaquamagnesium bis(8-anilino-1-naphthalenesulfonate) hexahydrate journal October 1977
The monoclinic structure of a fluorescent probe: ammonium 1-anilino-8-naphthalenesulfonate (ANS) monohydrate journal March 1980
A statistic for local intensity differences: robustness to anisotropy and pseudo-centering and utility for detecting twinning journal June 2003
Structure of a yellow lupin pathogenesis-related PR-10 protein belonging to a novel subclass journal December 2004
Scaling and assessment of data quality journal December 2005
Intensity statistics in twinned crystals with examples from the PDB journal December 2005
Surprises and pitfalls arising from (pseudo)symmetry journal December 2007
MolProbity : all-atom structure validation for macromolecular crystallography journal December 2009
REFMAC 5 for the refinement of macromolecular crystal structures journal March 2011
Intensity statistics in the presence of translational noncrystallographic symmetry journal January 2013
On the propagation of errors journal September 2013
The landscape of cytokinin binding by a plant nodulin journal November 2013
Likelihood-based molecular-replacement solution for a highly pathological crystal with tetartohedral twinning and sevenfold translational noncrystallographic symmetry journal January 2014
Specific binding of gibberellic acid by Cytokinin-Specific Binding Proteins: a new aspect of plant hormone-binding proteins with the PR-10 fold journal June 2014
Structural and functional aspects of PR-10 proteins journal February 2013
Structure-based analysis of thermodynamic and mechanical properties of cavity-containing proteins - case study of plant pathogenesis-related proteins of class 10 journal December 2013

Cited By (2)

Characterizing pathological imperfections in macromolecular crystals: lattice disorders and modulations journal December 2019
Supercell refinement: a cautionary tale journal August 2019

Similar Records

ANS complex of St John’s wort PR-10 protein with 28 copies in the asymmetric unit: a fiendish combination of pseudosymmetry with tetartohedral twinning
Journal Article · Wed Apr 01 00:00:00 EDT 2015 · Acta Crystallographica. Section D: Biological Crystallography · OSTI ID:22347699
Likelihood-based molecular-replacement solution for a highly pathological crystal with tetartohedral twinning and sevenfold translational noncrystallographic symmetry
Journal Article · Fri Jan 31 23:00:00 EST 2014 · Acta Crystallographica. Section D: Biological Crystallography · OSTI ID:22347780
Likelihood-based molecular-replacement solution for a highly pathological crystal with tetartohedral twinning and sevenfold translational noncrystallographic symmetry
Journal Article · Tue Jan 28 23:00:00 EST 2014 · Acta Crystallographica. Section D: Biological Crystallography (Online) · OSTI ID:1625712

Related Subjects

59 BASIC BIOLOGICAL SCIENCES
8-anilino-1-naphthalene sulfonate
Hypericum perforatum
St John’s wort
pathogenesis-related class 10 protein