1B7G | pdb_00001b7g

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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.05 Å
R-Value Free:
0.293 (Depositor), 0.266 (DCC)
R-Value Work:
0.226 (Depositor), 0.207 (DCC)

wwPDB Validation 3D Report Full Report

This is version 1.5 of the entry. See complete history.

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 Biology 291: 651-660

PubMed: 10448043 Search on PubMed
DOI: https://doi.org/10.1006/jmbi.1999.3003
Primary Citation 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.

Organizational Affiliation

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

Macromolecule Content

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

Macromolecules

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| 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P39460
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain C [auth O] SDF format, chain D [auth O] SDF format, chain E [auth O] SDF format, chain F [auth O] SDF format, chain G [auth O] SDF format, chain H [auth O] SDF format, chain I [auth Q] SDF format, chain J [auth Q] SDF format, chain K [auth Q] SDF format, chain L [auth Q] SDF format, chain M [auth Q] SDF format, chain N [auth Q] MOL2 format, chain C [auth O] MOL2 format, chain D [auth O] MOL2 format, chain E [auth O] MOL2 format, chain F [auth O] MOL2 format, chain G [auth O] MOL2 format, chain H [auth O] MOL2 format, chain I [auth Q] MOL2 format, chain J [auth Q] MOL2 format, chain K [auth Q] MOL2 format, chain L [auth Q] MOL2 format, chain M [auth Q] MOL2 format, chain N [auth Q] mmCIF format, chain C [auth O] mmCIF format, chain D [auth O] mmCIF format, chain E [auth O] mmCIF format, chain F [auth O] mmCIF format, chain G [auth O] mmCIF format, chain H [auth O] mmCIF format, chain I [auth Q] mmCIF format, chain J [auth Q] mmCIF format, chain K [auth Q] mmCIF format, chain L [auth Q] mmCIF format, chain M [auth Q] mmCIF format, chain N [auth Q]	C [auth O] D [auth O] E [auth O] F [auth O] G [auth O] 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		Interactions Focus chain C [auth O] Focus chain D [auth O] Focus chain E [auth O] Focus chain F [auth O] Focus chain G [auth O] Focus chain H [auth O] Focus chain I [auth Q] Focus chain J [auth Q] Focus chain K [auth Q] Focus chain L [auth Q] Focus chain M [auth Q] Focus chain N [auth Q] Interactions & Density Focus chain C [auth O] Focus chain D [auth O] Focus chain E [auth O] Focus chain F [auth O] Focus chain G [auth O] Focus chain H [auth O] Focus chain I [auth Q] Focus chain J [auth Q] Focus chain K [auth Q] Focus chain L [auth Q] Focus chain M [auth Q] Focus chain N [auth Q]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.05 Å
R-Value Free: 0.293 (Depositor), 0.266 (DCC)
R-Value Work: 0.226 (Depositor), 0.207 (DCC)

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

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Entry History

Deposition Data

Released Date: 1999-10-08

Deposition Author(s):

Isupov, M.N.

Littlechild, J.A.

Revision History (Full details and data files)

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