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CRYSTAL STRUCTURE OF NICOTIANA ALATA GEMETOPHYTIC SELF-INCOMPATIBILITY ASSOCIATED SF11-RNASE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.185 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The 1.55 A resolution structure of Nicotiana alata S(F11)-RNase associated with gametophytic self-incompatibility.

Ida, K.Norioka, S.Yamamoto, M.Kumasaka, T.Yamashita, E.Newbigin, E.Clarke, A.E.Sakiyama, F.Sato, M.

(2001) J.Mol.Biol. 314: 103-112

  • DOI: 10.1006/jmbi.2001.5127

  • PubMed Abstract: 
  • The crystal structure of Nicotiana alata (ornamental tobacco) S(F11)-RNase, an S-allelic glycoprotein associated with gametophytic self-incompatibility, was determined by X-ray diffraction at 1.55 A resolution. The protein has a tertiary structure ty ...

    The crystal structure of Nicotiana alata (ornamental tobacco) S(F11)-RNase, an S-allelic glycoprotein associated with gametophytic self-incompatibility, was determined by X-ray diffraction at 1.55 A resolution. The protein has a tertiary structure typical of members of the RNase T(2) family as it consists of a variant of the (alpha+beta) fold and has eight helices and seven strands. A heptasaccharide moiety is also present, and amino acid residues that serve as the catalytic acid and base can be assigned to His32 and His91, respectively. Two "hypervariable" regions, known as HVa and HVb, are the proposed sites of S-allele discrimination during the self-incompatibility reaction, and in the S(F11)-RNase these are well separated from the active site. HVa and HVb are composed of a long, positively charged loop followed by a part of an alpha-helix and short, negatively charged alpha-helix, respectively. The S(F11)-RNase structure shows both regions are readily accessible to the solvent and hence could participate in the process of self/non-self discrimination between the S-RNase and an unknown pollen S-gene product(s) upon pollination.


    Organizational Affiliation

    Graduate School of Integrated Science, Yokohama City University, Tsurumi-ku, Yokohama 230-0045, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
SF11-RNASE
A, B
196Nicotiana alataEC: 3.1.27.1
Find proteins for Q7SID5 (Nicotiana alata)
Go to UniProtKB:  Q7SID5
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MAN
Query on MAN

Download SDF File 
Download CCD File 
A, B
ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
BMA
Query on BMA

Download SDF File 
Download CCD File 
A, B
BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
A, B
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
XYP
Query on XYP

Download SDF File 
Download CCD File 
A, B
BETA-D-XYLOPYRANOSE
C5 H10 O5
SRBFZHDQGSBBOR-KKQCNMDGSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.185 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 65.869α = 90.00
b = 44.731β = 90.27
c = 64.360γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
MLPHAREphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-05-08
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Non-polymer description, Version format compliance