2PBZ | pdb_00002pbz

Crystal structure of an IMP biosynthesis protein PurP from Thermococcus kodakaraensis

• PDB DOI: https://doi.org/10.2210/pdb2PBZ/pdb

• Classification: LIGASE
• Organism(s): Thermococcus kodakarensis KOD1
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2007-03-29 Released: 2007-04-10 
• Deposition Author(s): Agarwal, R., Burley, S.K., Swaminathan, S., New York SGX Research Center for Structural Genomics (NYSGXRC)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.300 (Depositor), 0.310 (DCC) 
• R-Value Work: 
  0.276 (Depositor), 0.280 (DCC) 
• R-Value Observed: 
  0.276 (Depositor) 

Literature

Crystal structure of an IMP biosynthesis protein PurP from Thermococcus kodakaraensis

Agarwal, R., Burley, S.K., Swaminathan, S.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 111.28 kDa 
• Atom Count: 7,416 
• Modeled Residue Count: 879 
• Deposited Residue Count: 960 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hypothetical protein	A, B, C	320	Thermococcus kodakarensis KOD1	Mutation(s): 3  Gene Names: PurP, TK0431 EC: 6.3.4
UniProt
Find proteins for Q5JD28 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1)) Explore Q5JD28  Go to UniProtKB:  Q5JD28

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ATP	D [auth A], E [auth B], F [auth C]	ADENOSINE-5'-TRIPHOSPHATE C10 H16 N5 O13 P3 ZKHQWZAMYRWXGA-KQYNXXCUSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.300 (Depositor), 0.310 (DCC) 
• R-Value Work:  0.276 (Depositor), 0.280 (DCC) 
• R-Value Observed: 0.276 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.342	α = 90
b = 87.4	β = 90
c = 175.907	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling
SHARP	phasing
SHELXD	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-04-10 
Deposition Author(s): Agarwal, R., 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: Source and taxonomy, Version format compliance
• Version 1.3: 2021-02-03
  Changes: Database references, Derived calculations, Structure summary
• Version 1.4: 2024-11-20
  Changes: Data collection, Database references, Structure summary