3VUE

Crystal Structure of Rice Granule bound Starch Synthase I Catalytic Domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.218 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Interdomain Disulfide Bridge in the Rice Granule Bound Starch Synthase I Catalytic Domain as Elucidated by X-Ray Structure Analysis

Momma, M.Fujimoto, Z.

(2012) Biosci.Biotechnol.Biochem. 76: 1591-1595

  • DOI: 10.1271/bbb.120305
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The catalytic domain of rice (Oryza sativa japonica) granule bound starch synthase I (OsGBSSI-CD) was overexpressed and the three-dimensional structures of the ligand-free and ADP-bound forms were determined. The structures were similar to those repo ...

    The catalytic domain of rice (Oryza sativa japonica) granule bound starch synthase I (OsGBSSI-CD) was overexpressed and the three-dimensional structures of the ligand-free and ADP-bound forms were determined. The structures were similar to those reported for bacterial and archaeal glycogen synthases, which belong to glycosyltransferase family 5. They had Rossmann fold N- and C-domains connected by canonical two-hinge peptides, and an interdomain disulfide bond that appears to be conserved in the Poaceae plant family. The presence of three covalent linkages might explain why both OsGBSSI-CD structures adopted only the closed domain arrangement.


    Organizational Affiliation

    Biomolecular Research Unit, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan. momma@affrc.go.jp




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Granule-bound starch synthase 1, chloroplastic/amyloplastic
A
536Oryza sativa subsp. japonicaMutation(s): 0 
Gene Names: WAXY (WX, WX-B)
EC: 2.4.1.242
Find proteins for Q0DEV5 (Oryza sativa subsp. japonica)
Go to UniProtKB:  Q0DEV5
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.218 
  • Space Group: P 4 3 2
Unit Cell:
Length (Å)Angle (°)
a = 152.904α = 90.00
b = 152.904β = 90.00
c = 152.904γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data scaling
MOLREPphasing
ADSCdata collection
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-09-05
    Type: Initial release
  • Version 1.1: 2017-12-20
    Type: Database references