2CUN

Crystal structure of Phosphoglycerate Kinase from Pyrococcus horikoshii OT3

• PDB DOI: https://doi.org/10.2210/pdb2CUN/pdb

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


• Deposited: 2005-05-27 Released: 2005-06-14 
• Deposition Author(s): Mizutani, H., Kunishima, N., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.244 
• R-Value Work: 0.210 
• R-Value Observed: 0.210 

Starting Model: experimental

Literature

Crystal structure of Phosphoglycerate Kinase from Pyrococcus horikoshii OT3

Mizutani, H., Kunishima, N.

To be published.

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)

Macromolecule Content

• Total Structure Weight: 93.92 kDa 
• Atom Count: 6,890 
• Modelled Residue Count: 810 
• Deposited Residue Count: 820 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphoglycerate kinase	A, B	410	Pyrococcus horikoshii OT3	Mutation(s): 0  EC: 2.7.2.3
UniProt
Find proteins for O58965 (Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)) Explore O58965  Go to UniProtKB:  O58965

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
3PG	D [auth A], I [auth B]	3-PHOSPHOGLYCERIC ACID C3 H7 O7 P OSJPPGNTCRNQQC-UWTATZPHSA-N
MPD	F [auth A], G [auth A], K [auth B]	(4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N
GOL	E [auth A], J [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL	C [auth A], H [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.244 
• R-Value Work: 0.210 
• R-Value Observed: 0.210 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.854	α = 90
b = 123.327	β = 95.42
c = 82.943	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-06-14 
Deposition Author(s): Mizutani, H., Kunishima, N., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History  

• Version 1.0: 2005-06-14
  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