2YX5

Crystal Structure of Methanocaldococcus jannaschii PurS, One of the Subunits of Formylglycinamide Ribonucleotide Amidotransferase in the Purine Biosynthetic Pathway

• PDB DOI: https://doi.org/10.2210/pdb2YX5/pdb

• Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
• Organism(s): Methanocaldococcus jannaschii
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2007-04-24 Released: 2007-10-30 
• Deposition Author(s): Kanagawa, M., Baba, S., Agari, Y., Chen, L.Q., Fu, Z.-Q., Chrzas, J., Wang, B.C., Kuramitsu, S., Yokoyama, S., Kawai, G., Sampei, G., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.284 
• R-Value Work: 0.240 
• R-Value Observed: 0.240 

Starting Model: experimental

Literature

Crystal Structure of Methanocaldococcus jannaschii PurS, One of the Subunits of Formylglycinamide Ribonucleotide Amidotransferase in the Purine Biosynthetic Pathway

Kanagawa, M., Baba, S., Agari, Y., Chen, L.Q., Fu, Z.-Q., Chrzas, J., Wang, B.C., Kuramitsu, S., Yokoyama, S., Kawai, G., Sampei, G.

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,PQS (software)

Macromolecule Content

• Total Structure Weight: 9.71 kDa 
• Atom Count: 685 
• Modelled Residue Count: 82 
• Deposited Residue Count: 83 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UPF0062 protein MJ1593	A	83	Methanocaldococcus jannaschii	Mutation(s): 0  EC: 6.3.5.3
UniProt
Find proteins for Q58988 (Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440)) Explore Q58988  Go to UniProtKB:  Q58988

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.284 
• R-Value Work: 0.240 
• R-Value Observed: 0.240 
• Space Group: P 6₄ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 96.251	α = 90
b = 96.251	β = 90
c = 48.257	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-10-30 
Deposition Author(s): Kanagawa, M., Baba, S., Agari, Y., Chen, L.Q., Fu, Z.-Q., Chrzas, J., Wang, B.C., Kuramitsu, S., Yokoyama, S., Kawai, G., Sampei, G., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History  

• Version 1.0: 2007-10-30
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.2: 2023-10-25
  Changes: Data collection, Database references, Refinement description