1B7G

GLYCERALDEHYDE 3-PHOSPHATE DEHYDROGENASE

• PDB DOI: https://doi.org/10.2210/pdb1B7G/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Saccharolobus solfataricus
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 1999-01-22 Released: 1999-10-08 
• Deposition Author(s): Isupov, M.N., Littlechild, J.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 0.293 
• R-Value Work: 0.226 

Literature

Crystal structure of the glyceraldehyde-3-phosphate dehydrogenase from the hyperthermophilic archaeon Sulfolobus solfataricus.

Isupov, M.N., Fleming, T.M., Dalby, A.R., Crowhurst, G.S., Bourne, P.C., Littlechild, J.A.

(1999) J Mol Biol 291: 651-660

• PubMed: 10448043 
• DOI: https://doi.org/10.1006/jmbi.1999.3003
• Primary Citation of Related Structures:  
  1B7G


• PubMed Abstract: 
  

  The enzyme glyceraldehyde-3-phosphate dehydrogenase (GAPDH) from the archaea shows low sequence identity (16-20%) with its eubacterial and eukaryotic counterparts. The crystal structure of the apo GAPDH from Sulfolobus solfataricus has been determined by multiple isomorphous replacement at 2.05 A resolution. The enzyme has several differences in secondary structure when compared with eubacterial GAPDHs, with an overall increase in the number of alpha-helices. There is a relocation of the active-site residues within the catalytic domain of the enzyme. The thermostability of the S. solfataricus enzyme can be attributed to a combination of an ion pair cluster and an intrasubunit disulphide bond.

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Organizational Affiliation: 

Schools of Chemistry and Biological Sciences, University of Exeter, Stocker Road, Exeter, EX4 4QD, UK.

Biological Assembly 1  

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

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

Biological Assembly 2  

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

Biological assembly 2 generated by PISA,PQS (software)

Macromolecule Content

• Total Structure Weight: 76.42 kDa 
• Atom Count: 5,844 
• Modelled Residue Count: 680 
• Deposited Residue Count: 680 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN (GLYCERALDEHYDE 3-PHOSPHATE DEHYDROGENASE)	A [auth O], B [auth Q]	340	Saccharolobus solfataricus	Mutation(s): 1  EC: 1.2.1.12 (PDB Primary Data), 1.2.1.59 (UniProt)
UniProt
Find proteins for P39460 (Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2)) Explore P39460  Go to UniProtKB:  P39460

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 0.293 
• R-Value Work: 0.226 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 101.55	α = 90
b = 101.55	β = 90
c = 179.92	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SHELX	model building
MLPHARE	phasing
REFMAC	refinement
SHELX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1999-10-08 
Deposition Author(s): Isupov, M.N., Littlechild, J.A.

Revision History  

• Version 1.0: 1999-10-08
  Type: Initial release
  
• Version 1.1: 2007-10-16
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.3: 2021-11-03
  Changes: Database references, Derived calculations
• Version 1.4: 2023-12-27
  Changes: Data collection
• Version 1.5: 2024-10-30
  Changes: Structure summary