4TWM | pdb_00004twm

Crystal structure of dioscorin from Dioscorea japonica

• PDB DOI: https://doi.org/10.2210/pdb4TWM/pdb

• 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

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.11 Å
• R-Value Free: 
  0.272 (Depositor), 0.269 (DCC) 
• R-Value Work: 
  0.209 (Depositor), 0.208 (DCC) 
• R-Value Observed: 
  0.212 (Depositor) 

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

• PubMed: 25747844 
• DOI: https://doi.org/10.1016/j.molp.2015.02.015
• Primary Citation Related Structures: 
  4TWL, 4TWM

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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.
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.
Division of Molecular and Science, Faculty of Science and Technology, Gunma University, 1-5-1 Tenjin-cho, Kiryu, Gunma 376-8515, Japan.
Laboratory of Chemistry, College of Liberal Arts and Sciences, Tokyo Medical and Dental University, 2-8-30 Kounodai, Ichikawa-shi, Chiba 272-0827, Japan.
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. Electronic address: [e-mail].

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 3 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 56.63 kDa 
• Atom Count: 3,979 
• Modeled Residue Count: 475 
• Deposited Residue Count: 492 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dioscorin 5	A, B	246	Dioscorea japonica	Mutation(s): 1  Gene Names: dio5 EC: 4.2.1.1 (UniProt), 1.6.5.4 (UniProt)
UniProt
Find proteins for A7MAQ2 (Dioscorea japonica) Explore A7MAQ2  Go to UniProtKB:  A7MAQ2

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth A], D [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.11 Å
• R-Value Free:  0.272 (Depositor), 0.269 (DCC) 
• R-Value Work:  0.209 (Depositor), 0.208 (DCC) 
• R-Value Observed: 0.212 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 83.47	α = 90
b = 156.77	β = 90
c = 83.56	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2015-04-01 
Deposition Author(s): Xue, Y.L., Miyakawa, T., Nakamura, A., Tanokura, M.

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Funding Organization	Location	Grant Number
High Energy Accelerator Research Organization	Japan	2011G605
Targeted Proteins Research Program (TPRP) of the Ministry of Education, Culture, Sports, Science and Technology	Japan	--
National Natural Science Foundation of China	China	31201285
Scientific Research Foundation for the Returned Overseas Chinese Scholars	China	2013693

Revision History  

• 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: 2024-10-16
  Changes: Data collection, Database references, Structure summary