1V6S | pdb_00001v6s

Crystal Structure of Phosphoglycerate Kinase from Thermus thermophilus HB8

• PDB DOI: https://doi.org/10.2210/pdb1V6S/pdb

• Classification: TRANSFERASE
• Organism(s): Thermus thermophilus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2003-12-04 Released: 2003-12-23 
• Deposition Author(s): Mizutani, H., Kunishima, N., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 
  0.215 (Depositor), 0.197 (DCC) 
• R-Value Work: 
  0.201 (Depositor), 0.198 (DCC) 
• R-Value Observed: 
  0.202 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of Phosphoglycerate Kinase from Thermus thermophilus HB8

Mizutani, H., Kunishima, N.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 84.1 kDa 
• Atom Count: 6,659 
• Modeled Residue Count: 780 
• Deposited Residue Count: 780 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphoglycerate kinase	A, B	390	Thermus thermophilus	Mutation(s): 0  EC: 2.7.2.3
UniProt
Find proteins for P09403 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore P09403  Go to UniProtKB:  P09403

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	D [auth A], E [auth A], H [auth B], I [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
NA	C [auth A], F [auth B], G [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free:  0.215 (Depositor), 0.197 (DCC) 
• R-Value Work:  0.201 (Depositor), 0.198 (DCC) 
• R-Value Observed: 0.202 (Depositor) 

Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 143.175	α = 90
b = 143.175	β = 90
c = 75.641	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2003-12-23 
Deposition Author(s): Mizutani, H., Kunishima, N., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History  

• Version 1.0: 2003-12-23
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.3: 2023-10-25
  Changes: Data collection, Database references, Derived calculations, Refinement description