3VUF

Crystal Structure of Rice Granule bound Starch Synthase I Catalytic Domain in Complex with ADP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.224 

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:  
    3VUE, 3VUF

  • 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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Granule-bound starch synthase 1, chloroplastic/amyloplasticA536Oryza sativa Japonica GroupMutation(s): 0 
Gene Names: WAXYWXWX-BOs06g0133000LOC_Os06g04200134P10.7P0679C08.19
EC: 2.4.1.242
Find proteins for Q0DEV5 (Oryza sativa subsp. japonica)
Explore Q0DEV5 
Go to UniProtKB:  Q0DEV5
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ADP
Query on ADP

Download CCD File 
A
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
SO4
Query on SO4

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.224 
  • Space Group: P 4 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 153.368α = 90
b = 153.368β = 90
c = 153.368γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

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