3VUF | pdb_00003vuf

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

• PDB DOI: https://doi.org/10.2210/pdb3VUF/pdb

• Classification: TRANSFERASE
• Organism(s): Oryza sativa Japonica Group
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2012-06-28 Released: 2012-09-05 
• Deposition Author(s): Momma, M., Fujimoto, Z.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 
  0.271 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.221 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.224 (Depositor) 

Starting Model: experimental

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

• PubMed: 22878205 
• DOI: https://doi.org/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 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. [e-mail]

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 60.07 kDa 
• Atom Count: 3,864 
• Modelled Residue Count: 488 
• Deposited Residue Count: 536 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Granule-bound starch synthase 1, chloroplastic/amyloplastic	A	536	Oryza sativa Japonica Group	Mutation(s): 0  Gene Names: WAXY, WX, WX-B, Os06g0133000, LOC_Os06g04200, 134P10.7, P0679C08.19 EC: 2.4.1.242
UniProt
Find proteins for Q0DEV5 (Oryza sativa subsp. japonica) Explore Q0DEV5  Go to UniProtKB:  Q0DEV5

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ADP	B [auth A]	ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N
SO4	C [auth A], D [auth A], E [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free:  0.271 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.221 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.224 (Depositor) 

Space Group: P 4 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 153.368	α = 90
b = 153.368	β = 90
c = 153.368	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-09-05 
Deposition Author(s): Momma, M., Fujimoto, Z.

Revision History  

• Version 1.0: 2012-09-05
  Type: Initial release
  
• Version 1.1: 2017-12-20
  Changes: Database references
• Version 1.2: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.3: 2024-11-20
  Changes: Structure summary