4TWL

Crystal structure of dioscorin complexed with ascorbate

  • Classification: PLANT PROTEIN
  • Organism(s): Dioscorea japonica
  • Expression System: Escherichia coli
  • Mutation(s): Yes 

  • Deposited: 2014-07-01 Released: 2015-04-01 
  • Deposition Author(s): Xue, Y.L., Miyakawa, T., Nakamura, A., Tanokura, M.
  • Funding Organization(s): High Energy Accelerator Research Organization, Targeted Proteins Research Program (TPRP) of the Ministry of Education, Culture, Sports, Science and Technology of Japan, National Natural Science Foundation of China, Scientific Research Foundation for the Returned Overseas Chinese Scholars

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.11 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.205 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Yam Tuber Storage Protein Reduces Plant Oxidants Using the Coupled Reactions as Carbonic Anhydrase and Dehydroascorbate Reductase

Xue, Y.L.Miyakawa, T.Nakamura, A.Hatano, K.Sawano, Y.Tanokura, M.

(2015) Mol Plant 8: 1115-1118

  • DOI: https://doi.org/10.1016/j.molp.2015.02.015
  • Primary Citation of Related Structures:  
    4TWL, 4TWM

  • Organizational Affiliation

    Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan; College of Light Industry, Liaoning University, 66 Chongshan Middle Road, Shenyang 110036, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Dioscorin 5
A, B
246Dioscorea japonicaMutation(s): 1 
Gene Names: dio5
UniProt
Find proteins for A7MAQ2 (Dioscorea japonica)
Explore A7MAQ2 
Go to UniProtKB:  A7MAQ2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA7MAQ2
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.11 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.205 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 83.505α = 90
b = 157.103β = 90
c = 83.485γ = 90
Software Package:
Software NamePurpose
REFMACrefinement

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
High Energy Accelerator Research OrganizationJapan2011G605
Targeted Proteins Research Program (TPRP) of the Ministry of Education, Culture, Sports, Science and Technology of JapanJapan--
National Natural Science Foundation of ChinaChina31201285
Scientific Research Foundation for the Returned Overseas Chinese ScholarsChina2013693

Revision History  (Full details and data files)

  • Version 1.0: 2015-04-01
    Type: Initial release
  • Version 1.1: 2015-08-05
    Changes: Database references
  • Version 1.2: 2020-01-29
    Changes: Data collection, Derived calculations
  • Version 1.3: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations