4TWM

Crystal structure of dioscorin from Dioscorea japonica

  • 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, 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: 0.272 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.212 

wwPDB Validation   3D Report Full Report


This is version 1.2 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: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Dioscorin 5A, B246Dioscorea japonicaMutation(s): 1 
Gene Names: dio5, dioA3
EC: 1.6.5.4 (UniProt), 4.2.1.1 (UniProt)
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
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4
Download Ideal Coordinates CCD File 
C [auth A],
D [auth A]		SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.11 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.212 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 83.47α = 90
b = 156.77β = 90
c = 83.56γ = 90
Software Package:
Software NamePurpose
REFMACrefinement

Structure Validation

View Full Validation Report



View more in-depth experimental data
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 TechnologyJapan--
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