2IJ9 | pdb_00002ij9

Crystal Structure of Uridylate Kinase from Archaeoglobus Fulgidus

• PDB DOI: https://doi.org/10.2210/pdb2IJ9/pdb

• Classification: TRANSFERASE
• Organism(s): Archaeoglobus fulgidus DSM 4304
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2006-09-29 Released: 2006-10-17 
• Deposition Author(s): Patskovsky, Y., Chen, R., Keefe, L.J., Sauder, J.M., Dickey, M., Adams, J.M., Ozyurt, S., Wasserman, S.R., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 
  0.330 (Depositor), 0.301 (DCC) 
• R-Value Work: 
  0.283 (Depositor) 
• R-Value Observed: 
  0.284 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of Uridylate Kinase from Archaeoglobus Fulgidus

Patskovsky, Y., Chen, R., Keefe, L.J., Sauder, J.M., Dickey, M., Adams, J.M., Ozyurt, S., Wasserman, S.R., Burley, S.K., Almo, S.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.

Macromolecule Content 

• Total Structure Weight: 46.9 kDa 
• Atom Count: 3,234 
• Modeled Residue Count: 430 
• Deposited Residue Count: 438 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uridylate kinase	A, B	219	Archaeoglobus fulgidus DSM 4304	Mutation(s): 1  Gene Names: pyrH, AF_2042 EC: 2.7.4 (PDB Primary Data), 2.7.4.22 (UniProt)
UniProt
Find proteins for O28237 (Archaeoglobus fulgidus (strain ATCC 49558 / DSM 4304 / JCM 9628 / NBRC 100126 / VC-16)) Explore O28237  Go to UniProtKB:  O28237

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free:  0.330 (Depositor), 0.301 (DCC) 
• R-Value Work:  0.283 (Depositor) 
• R-Value Observed: 0.284 (Depositor) 

Space Group: P 4₃ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 94.277	α = 90
b = 94.277	β = 90
c = 186.672	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-10-17 
Deposition Author(s): Patskovsky, Y., Chen, R., Keefe, L.J., Sauder, J.M., Dickey, M., Adams, J.M., Ozyurt, S., Wasserman, S.R., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2006-10-17
  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: 2018-11-14
  Changes: Data collection, Structure summary
• Version 1.4: 2021-02-03
  Changes: Database references, Derived calculations, Structure summary
• Version 1.5: 2021-10-20
  Changes: Database references
• Version 1.6: 2023-08-30
  Changes: Data collection, Refinement description