2CZC | pdb_00002czc

Crystal structure of glyceraldehyde-3-phosphate dehydrogenase from Pyrococcus horikoshii OT3

• PDB DOI: https://doi.org/10.2210/pdb2CZC/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Pyrococcus horikoshii OT3
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2005-07-13 Released: 2006-01-13 
• Deposition Author(s): Ito, K., Arai, R., Kamo-Uchikubo, T., Shirouzu, M., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.241 (Depositor), 0.242 (DCC) 
• R-Value Work: 
  0.205 (Depositor), 0.207 (DCC) 

Starting Model: experimental

Literature

Crystal structure of glyceraldehyde-3-phosphate dehydrogenase from Pyrococcus horikoshii OT3

Ito, K., Arai, R., Kamo-Uchikubo, T., Shirouzu, M., Yokoyama, S.

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: 152.38 kDa 
• Atom Count: 11,153 
• Modeled Residue Count: 1,332 
• Deposited Residue Count: 1,336 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glyceraldehyde-3-phosphate dehydrogenase	A, B, C, D	334	Pyrococcus horikoshii OT3	Mutation(s): 0  Gene Names: PH1830 EC: 1.2.1.59
UniProt
Find proteins for O59494 (Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)) Explore O59494  Go to UniProtKB:  O59494

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAD	G [auth A], I [auth B], K [auth C], M [auth D]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C21 H27 N7 O14 P2 BAWFJGJZGIEFAR-NNYOXOHSSA-N
PO4	E [auth A], F [auth A], H [auth B], J [auth C], L [auth D]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.241 (Depositor), 0.242 (DCC) 
• R-Value Work:  0.205 (Depositor), 0.207 (DCC) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.693	α = 90
b = 127.192	β = 90
c = 161.454	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-01-13 
Deposition Author(s): Ito, K., Arai, R., Kamo-Uchikubo, T., Shirouzu, M., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History  

• Version 1.0: 2006-01-13
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.3: 2023-10-25
  Changes: Data collection, Database references, Derived calculations, Refinement description