4TWL

Crystal structure of dioscorin complexed with ascorbate

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

  • 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 

wwPDB Validation 3D Report Full Report


This is version 1.1 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


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Dioscorin 5
A, B
246Dioscorea japonicaMutation(s): 1 
Gene Names: dio5
Find proteins for A7MAQ2 (Dioscorea japonica)
Go to UniProtKB:  A7MAQ2
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
ASC
Query on ASC

Download SDF File 
Download CCD File 
A, B
ASCORBIC ACID
C6 H8 O6
CIWBSHSKHKDKBQ-JLAZNSOCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.11 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.201 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 83.505α = 90.00
b = 157.103β = 90.00
c = 83.485γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationCountryGrant 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 

  • Version 1.0: 2015-04-01
    Type: Initial release
  • Version 1.1: 2015-08-05
    Type: Database references