3QTG | pdb_00003qtg

Crystal structure of pyruvate kinase from Pyrobaculum aerophilum

• PDB DOI: https://doi.org/10.2210/pdb3QTG/pdb

• Classification: TRANSFERASE
• Organism(s): Pyrobaculum aerophilum str. IM2
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2011-02-22 Released: 2012-02-22 
• Deposition Author(s): Davies, C., Solomons, J.T.G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.247 (Depositor), 0.248 (DCC) 
• R-Value Work: 
  0.206 (Depositor), 0.204 (DCC) 
• R-Value Observed: 
  0.208 (Depositor) 

Starting Model: experimental

Literature

The crystal structure of pyruvate kinase from the hyperthermophilic archaeon Pyrobaculum aerophilum: insights into cooperative regulation

Solomons, J.T.G., Johnson, U., Schoenheit, P., Davies, C.

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: 100.93 kDa 
• Atom Count: 6,889 
• Modeled Residue Count: 869 
• Deposited Residue Count: 922 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Pyruvate kinase	A, B	461	Pyrobaculum aerophilum str. IM2	Mutation(s): 0  Gene Names: PAE0819, pyk EC: 2.7.1.40
UniProt
Find proteins for Q8ZYE0 (Pyrobaculum aerophilum (strain ATCC 51768 / DSM 7523 / JCM 9630 / CIP 104966 / NBRC 100827 / IM2)) Explore Q8ZYE0  Go to UniProtKB:  Q8ZYE0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth A], D [auth B], E [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.247 (Depositor), 0.248 (DCC) 
• R-Value Work:  0.206 (Depositor), 0.204 (DCC) 
• R-Value Observed: 0.208 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 116.3	α = 90
b = 107.4	β = 110.5
c = 105	γ = 90

Software Package:

Software Name	Purpose
MAR345	data collection
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-02-22 
Deposition Author(s): Davies, C., Solomons, J.T.G.

Revision History  

• Version 1.0: 2012-02-22
  Type: Initial release
  
• Version 1.1: 2017-11-08
  Changes: Refinement description
• Version 1.2: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description