2G82 | pdb_00002g82

High Resolution Structures of Thermus aquaticus Glyceraldehyde-3-Phosphate Dehydrogenase: Role of 220's Loop Motion in Catalysis

• PDB DOI: https://doi.org/10.2210/pdb2G82/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Thermus aquaticus
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2006-03-01 Released: 2007-03-13 
• Deposition Author(s): Jenkins, J.L., Buencamino, R., Tanner, J.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 
  0.172 (Depositor), 0.176 (DCC) 
• R-Value Work: 
  0.158 (Depositor), 0.164 (DCC) 

Starting Model: experimental

Literature

High Resolution Structures of Thermus aquaticus Glyceraldehyde-3-Phosphate Dehydrogenase: Role of 220's Loop Motion in Catalysis

Jenkins, J.L., Buencamino, R., Tanner, J.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 PQS (software)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PQS (software)

Macromolecule Content 

• Total Structure Weight: 293.66 kDa 
• Atom Count: 22,023 
• Modeled Residue Count: 2,640 
• Deposited Residue Count: 2,648 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glyceraldehyde-3-phosphate dehydrogenase	A [auth O], B [auth P], C [auth Q], D [auth R], E [auth A], F [auth B], G [auth C], H [auth D]	331	Thermus aquaticus	Mutation(s): 1  Gene Names: gap EC: 1.2.1.12
UniProt
Find proteins for P00361 (Thermus aquaticus) Explore P00361  Go to UniProtKB:  P00361

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAD	I [auth O], J [auth P], K [auth Q], N [auth R], P [auth A], Q [auth B], S [auth C], V [auth D]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C21 H27 N7 O14 P2 BAWFJGJZGIEFAR-NNYOXOHSSA-N
PGE	T [auth C]	TRIETHYLENE GLYCOL C6 H14 O4 ZIBGPFATKBEMQZ-UHFFFAOYSA-N
GOL	M [auth Q], O [auth R], W [auth D]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
IPA	L [auth Q], U [auth C]	ISOPROPYL ALCOHOL C3 H8 O KFZMGEQAYNKOFK-UHFFFAOYSA-N
NA	R [auth C]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSD	A [auth O], B [auth P], C [auth Q], D [auth R], E [auth A], F [auth B], G [auth C], H [auth D]	L-PEPTIDE LINKING	C3 H7 N O4 S		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free:  0.172 (Depositor), 0.176 (DCC) 
• R-Value Work:  0.158 (Depositor), 0.164 (DCC) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 141.549	α = 90
b = 147.403	β = 90
c = 147.669	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
SCALEPACK	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-03-13 
Deposition Author(s): Jenkins, J.L., Buencamino, R., Tanner, J.J.

Revision History  

• Version 1.0: 2007-03-13
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Derived calculations, Refinement description, Version format compliance
• Version 1.3: 2014-11-12
  Changes: Non-polymer description
• Version 1.4: 2023-08-30
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.5: 2024-10-30
  Changes: Structure summary