3E6A | pdb_00003e6a

Crystal structure and Functional Analysis of Glyceraldehyde-3-phosphate Dehydrogenase from Oryza Sativa

• PDB DOI: https://doi.org/10.2210/pdb3E6A/pdb

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


• Deposited: 2008-08-15 Released: 2009-08-18 
• Deposition Author(s): Tien, Y.C., Lin, Y.H., Chang, S.L., Chen, C.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.77 Å
• R-Value Free: 
  0.210 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.196 (Depositor), 0.220 (DCC) 

Literature

Crystal structure and Functional Analysis of Glyceraldehyde-3-phosphate Dehydrogenase from Oryza Sativa

Tien, Y.C., Lin, Y.H., Chang, S.L., Chen, C.J.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Macromolecule Content 

• Total Structure Weight: 146.08 kDa 
• Atom Count: 10,312 
• Modeled Residue Count: 1,339 
• Deposited Residue Count: 1,344 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glyceraldehyde-3-phosphate dehydrogenase, cytosolic	A [auth O], B [auth A], C [auth B], D [auth C]	336	Oryza sativa Japonica Group	Mutation(s): 0  Gene Names: GAPDH EC: 1.2.1.12
UniProt
Find proteins for Q0J8A4 (Oryza sativa subsp. japonica) Explore Q0J8A4  Go to UniProtKB:  Q0J8A4

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	E [auth O], F [auth O], G [auth A], H [auth A], I [auth B], J [auth B], K [auth C], L [auth C]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.77 Å
• R-Value Free:  0.210 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.196 (Depositor), 0.220 (DCC) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.258	α = 90
b = 127.418	β = 118.05
c = 77.385	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-08-18 
Deposition Author(s): Tien, Y.C., Lin, Y.H., Chang, S.L., Chen, C.J.

Revision History  

• Version 1.0: 2009-08-18
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2024-03-20
  Changes: Data collection, Database references