2PB9 | pdb_00002pb9

Crystal structure of C-terminal domain of phosphomethylpyrimidine kinase

• PDB DOI: https://doi.org/10.2210/pdb2PB9/pdb

• Classification: TRANSFERASE
• Organism(s): Pyrococcus furiosus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2007-03-28 Released: 2007-04-10 
• Deposition Author(s): Eswaramoorthy, S., Burley, S.K., Swaminathan, S., New York SGX Research Center for Structural Genomics (NYSGXRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 
  0.291 (Depositor), 0.290 (DCC) 
• R-Value Work: 
  0.234 (Depositor), 0.240 (DCC) 
• R-Value Observed: 
  0.234 (Depositor) 

Literature

Crystal structure of C-terminal domain of phosphomethylpyrimidine kinase

Eswaramoorthy, S., Burley, S.K., Swaminathan, 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.

Macromolecule Content 

• Total Structure Weight: 45.93 kDa 
• Atom Count: 3,005 
• Modeled Residue Count: 368 
• Deposited Residue Count: 390 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphomethylpyrimidine kinase	A, B	195	Pyrococcus furiosus	Mutation(s): 3  Gene Names: PF1333 EC: 2.7.1.49 (UniProt), 2.5.1.3 (UniProt), 2.7.4.7 (UniProt)
UniProt
Find proteins for Q8U193 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)) Explore Q8U193  Go to UniProtKB:  Q8U193

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	C [auth A], D [auth B]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free:  0.291 (Depositor), 0.290 (DCC) 
• R-Value Work:  0.234 (Depositor), 0.240 (DCC) 
• R-Value Observed: 0.234 (Depositor) 

Space Group: P 4₂ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.126	α = 90
b = 78.126	β = 90
c = 155.388	γ = 90

Software Package:

Software Name	Purpose
CBASS	data collection
SOLVE	phasing
SHARP	phasing
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-04-10 
Deposition Author(s): Eswaramoorthy, S., Burley, S.K., Swaminathan, S., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2007-04-10
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2021-02-03
  Changes: Database references, Derived calculations, Structure summary
• Version 1.4: 2024-10-30
  Changes: Data collection, Database references, Structure summary