4IQ8 | pdb_00004iq8

Crystal structure of glyceraldehyde-3-phosphate dehydrogenase 3 from Saccharomyces cerevisiae

• PDB DOI: https://doi.org/10.2210/pdb4IQ8/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Saccharomyces cerevisiae S288C
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2013-01-11 Released: 2013-02-06 
• Deposition Author(s): Wang, H., Liu, Q., Niu, L., Teng, M., Li, X.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.49 Å
• R-Value Free: 
  0.274 (Depositor), 0.259 (DCC) 
• R-Value Work: 
  0.214 (Depositor), 0.204 (DCC) 
• R-Value Observed: 
  0.217 (Depositor) 

Starting Model: experimental

Literature

Preliminary crystallographic analysis of glyceraldehyde-3-phosphate dehydrogenase 3 from Saccharomyces cerevisiae.

Liu, Q., Wang, H., Liu, H., Teng, M., Li, X.

(2012) Acta Crystallogr Sect F Struct Biol Cryst Commun 68: 978-980

• PubMed: 22869137 
• DOI: https://doi.org/10.1107/S1744309112028989
• Primary Citation Related Structures: 
  4IQ8


• PubMed Abstract: 
  

  Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) is an important enzyme in the glycolytic pathway. In addition to its conventional metabolic role, GAPDH has been identified to possess diverse cellular functions. In this study, glyceraldehyde-3-phosphate dehydrogenase 3, the third isoform of GAPDH from Saccharomyces cerevisiae, was cloned, expressed, purified and crystallized. The crystals belonged to space group I4(1)22, with unit-cell parameters a = b = 116.13, c = 119.21 Å. X-ray diffraction data were collected to a resolution of 2.6 Å. The structure was solved by molecular replacement and refinement is in progress.

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Organizational Affiliation: 
• School of Life Sciences, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui 230026, People's Republic of China.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 generated by PISA (software)

Biological Assembly 3  

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

Biological assembly 3 generated by PISA (software)

Biological Assembly 4  

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

Biological assembly 4 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 36.81 kDa 
• Atom Count: 2,521 
• Modeled Residue Count: 331 
• Deposited Residue Count: 340 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glyceraldehyde-3-phosphate dehydrogenase 3	A	340	Saccharomyces cerevisiae S288C	Mutation(s): 0  Gene Names: TDH3, GPD3, YGR192C, G7576 EC: 1.2.1.12
UniProt
Find proteins for P00359 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P00359  Go to UniProtKB:  P00359

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.49 Å
• R-Value Free:  0.274 (Depositor), 0.259 (DCC) 
• R-Value Work:  0.214 (Depositor), 0.204 (DCC) 
• R-Value Observed: 0.217 (Depositor) 

Space Group: I 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 116.129	α = 90
b = 116.129	β = 90
c = 119.179	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-02-06 
Deposition Author(s): Wang, H., Liu, Q., Niu, L., Teng, M., Li, X.

Revision History  

• Version 1.0: 2013-02-06
  Type: Initial release
  
• Version 1.1: 2023-09-20
  Changes: Data collection, Database references, Refinement description