2JI5 | pdb_00002ji5

Structure of UMP kinase from Pyrococcus furiosus complexed with UTP

• PDB DOI: https://doi.org/10.2210/pdb2JI5/pdb

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


• Deposited: 2007-02-26 Released: 2007-10-16 
• Deposition Author(s): Marco-Marin, C., Rubio, V.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.45 Å
• R-Value Free: 
  0.254 (Depositor) 
• R-Value Work: 
  0.209 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.209 (Depositor) 

Starting Model: experimental

Literature

The Structure of Ump Kinase from Pyrococcus Furiosus Complexed with Utp

Marco-Marin, C., Rubio, V.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D3  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

Biological assembly 1 generated by PQS (software)

Macromolecule Content 

• Total Structure Weight: 50.5 kDa 
• Atom Count: 3,368 
• Modeled Residue Count: 431 
• Deposited Residue Count: 454 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
URIDYLATE KINASE	A, B	227	Pyrococcus furiosus	Mutation(s): 1  EC: 2.7.4 (PDB Primary Data), 2.7.4.22 (UniProt)
UniProt
Find proteins for Q8U122 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)) Explore Q8U122  Go to UniProtKB:  Q8U122

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
UTP	C [auth A], D [auth B]	URIDINE 5'-TRIPHOSPHATE C9 H15 N2 O15 P3 PGAVKCOVUIYSFO-XVFCMESISA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.45 Å
• R-Value Free:  0.254 (Depositor) 
• R-Value Work:  0.209 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.209 (Depositor) 

Space Group: I 2 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 144.943	α = 90
b = 144.943	β = 90
c = 144.943	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-10-16 
Deposition Author(s): Marco-Marin, C., Rubio, V.

Revision History  

• Version 1.0: 2007-10-16
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-12-13
  Changes: Data collection, Database references, Other, Refinement description