2XRF | pdb_00002xrf

Crystal structure of human uridine phosphorylase 2

• PDB DOI: https://doi.org/10.2210/pdb2XRF/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2010-09-14 Released: 2010-09-29 
• Deposition Author(s): Welin, M., Moche, M., Arrowsmith, C.H., Berglund, H., Bountra, C., Collins, R., Edwards, A.M., Flodin, S., Flores, A., Graslund, S., Hammarstrom, M., Johansson, I., Karlberg, T., Kol, S., Kotenyova, T., Kouznetsova, E., Nyman, T., Persson, C., Schuler, H., Schutz, P., Siponen, M.I., Thorsell, A.G., Tresaugues, L., Van Der Berg, S., Wahlberg, E., Weigelt, J., Nordlund, P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.206 (Depositor), 0.168 (DCC) 
• R-Value Work: 
  0.168 (Depositor), 0.164 (DCC) 
• R-Value Observed: 
  0.170 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of Human Uridine Phosphorylase 2

Welin, M., Moche, M., Arrowsmith, C.H., Berglund, H., Bountra, C., Collins, R., Edwards, A.M., Flodin, S., Flores, A., Graslund, S., Hammarstrom, M., Johansson, I., Karlberg, T., Kol, S., Kotenyova, T., Kouznetsova, E., Nyman, T., Persson, C., Schuler, H., Schutz, P., Siponen, M.I., Thorsell, A.G., Tresaugues, L., Van Der Berg, S., Wahlberg, E., Weigelt, J., Nordlund, P.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 103.22 kDa 
• Atom Count: 7,274 
• Modeled Residue Count: 863 
• Deposited Residue Count: 909 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
URIDINE PHOSPHORYLASE 2	A, B, C	303	Homo sapiens	Mutation(s): 0  EC: 2.4.2.3
UniProt & NIH Common Fund Data Resources
Find proteins for O95045 (Homo sapiens) Explore O95045  Go to UniProtKB:  O95045
PHAROS:  O95045 GTEx:  ENSG00000007001

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
URA	E [auth A], H [auth B], K [auth C]	URACIL C4 H4 N2 O2 ISAKRJDGNUQOIC-UHFFFAOYSA-N
GOL	F [auth A], I [auth B], L [auth C]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
MG	D [auth A], G [auth B], J [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.206 (Depositor), 0.168 (DCC) 
• R-Value Work:  0.168 (Depositor), 0.164 (DCC) 
• R-Value Observed: 0.170 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 95.28	α = 90
b = 95.28	β = 90
c = 186.28	γ = 120

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-09-29 
Deposition Author(s): Welin, M., Moche, M., Arrowsmith, C.H., Berglund, H., Bountra, C., Collins, R., Edwards, A.M., Flodin, S., Flores, A., Graslund, S., Hammarstrom, M., Johansson, I., Karlberg, T., Kol, S., Kotenyova, T., Kouznetsova, E., Nyman, T., Persson, C., Schuler, H., Schutz, P., Siponen, M.I., Thorsell, A.G., Tresaugues, L., Van Der Berg, S., Wahlberg, E., Weigelt, J., Nordlund, P.

Revision History  

• Version 1.0: 2010-09-29
  Type: Initial release
  
• Version 1.1: 2013-11-27
  Changes: Non-polymer description, Source and taxonomy, Version format compliance
• Version 1.2: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description