1K3F | pdb_00001k3f

Uridine Phosphorylase from E. coli, Refined in the Monoclinic Crystal Lattice

• PDB DOI: https://doi.org/10.2210/pdb1K3F/pdb

• Classification: TRANSFERASE
• Organism(s): Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2001-10-02 Released: 2001-10-10 
• Deposition Author(s): Morgunova, E.Yu., Mikhailov, A.M., Popov, A.N., Blagova, E.V., Smirnova, E.A., Vainshtein, B.K., Mao, C., Armstrong, S.R., Ealick, S.E., Komissarov, A.A., Linkova, E.V., Burlakova, A.A., Mironov, A.S., Debabov, V.G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Work: 
  0.186 (Depositor) 

Starting Model: experimental

Literature

Atomic structure at 2.5 A resolution of uridine phosphorylase from E. coli as refined in the monoclinic crystal lattice.

Morgunova, E.Yu., Mikhailov, A.M., Popov, A.N., Blagova, E.V., Smirnova, E.A., Vainshtein, B.K., Mao, C., Armstrong, S.R., Ealick, S.E., Komissarov, A.A., Linkova, E.V., Burlakova, A.A., Mironov, A.S., Debabov, V.G.

(1995) FEBS Lett 367: 183-187

• PubMed: 7796917 
• DOI: https://doi.org/10.1016/0014-5793(95)00489-v
• Primary Citation Related Structures: 
  1K3F


• PubMed Abstract: 
  

  Uridine phosphorylase from E. coli (Upase) has been crystallized using vapor diffusion technique in a new monoclinic crystal form. The structure was determined by the molecular replacement method at 2.5 A resolution. The coordinates of the trigonal crystal form were used as a starting model and the refinement by the program XPLOR led to the R-factor of 18.6%. The amino acid fold of the protein was found to be the same as that in the trigonal crystals. The positions of flexible regions were refined. The conclusion about the involvement in the active site is in good agreement with the results of the biochemical experiments.

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Organizational Affiliation: 
• Institute of Crystallography of Russian Academy of Sciences, Moscow.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 163.13 kDa 
• Atom Count: 11,286 
• Modeled Residue Count: 1,518 
• Deposited Residue Count: 1,518 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
uridine phosphorylase	A, B, C, D, E, F	253	Escherichia coli	Mutation(s): 0  EC: 2.4.2.3
UniProt
Find proteins for P12758 (Escherichia coli (strain K12)) Explore P12758  Go to UniProtKB:  P12758

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Work:  0.186 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 92.6	α = 90
b = 98.8	β = 120.2
c = 93.7	γ = 90

Software Package:

Software Name	Purpose
AMoRE	phasing
X-PLOR	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2001-10-10 
Deposition Author(s): Morgunova, E.Yu., Mikhailov, A.M., Popov, A.N., Blagova, E.V., Smirnova, E.A., Vainshtein, B.K., Mao, C., Armstrong, S.R., Ealick, S.E., Komissarov, A.A., Linkova, E.V., Burlakova, A.A., Mironov, A.S., Debabov, V.G.

Revision History  

• Version 1.0: 2001-10-10
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-02-07
  Changes: Data collection, Database references, Refinement description
• Version 1.4: 2024-04-03
  Changes: Refinement description