8CSO

Crystal Structure of Orotidine 5'-phosphate decarboxylase from Klebsiella pneumoniae in complex with Uridine-5'-monophosphate

• PDB DOI: https://doi.org/10.2210/pdb8CSO/pdb

• Classification: LYASE
• Organism(s): Klebsiella pneumoniae subsp. pneumoniae HS11286
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2022-05-13 Released: 2022-06-08 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease, Seattle Structural Genomics Center for Infectious Disease (SSGCID)
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.235 
• R-Value Work: 0.197 
• R-Value Observed: 0.198 

Literature

Crystal Structure of Orotidine 5'-phosphate decarboxylase from Klebsiella pneumoniae in complex with Guanosine-5'-monophosphate

Abendroth, J., Davies, D.R., Lorimer, D.D., Horanyi, P.S., Edwards, T.E.

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.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Biological Assembly 3  

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

Biological assembly 3 assigned by authors.

Biological Assembly 4  

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

Biological assembly 4 assigned by authors.

Biological Assembly 5  

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

Biological assembly 5 assigned by authors.

Macromolecule Content

• Total Structure Weight: 258.67 kDa 
• Atom Count: 16,033 
• Modelled Residue Count: 2,191 
• Deposited Residue Count: 2,360 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Orotidine 5'-phosphate decarboxylase	A, B, C, D, E, F, G, H, I, J	236	Klebsiella pneumoniae subsp. pneumoniae HS11286	Mutation(s): 0  Gene Names: pyrF, KPHS_21850 EC: 4.1.1.23
UniProt
Find proteins for A0A0H3GNE4 (Klebsiella pneumoniae subsp. pneumoniae (strain HS11286)) Explore A0A0H3GNE4  Go to UniProtKB:  A0A0H3GNE4

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
U5P (Subject of Investigation/LOI)	K [auth A], L [auth B], N [auth C], P [auth E], R [auth F]	URIDINE-5'-MONOPHOSPHATE C9 H13 N2 O9 P DJJCXFVJDGTHFX-XVFCMESISA-N
EDO	M [auth B], O [auth C], Q [auth F]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.235 
• R-Value Work: 0.197 
• R-Value Observed: 0.198 
• Space Group: P 1
• Diffraction Data: https://doi.org/10.18430/M38CSO

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.71	α = 100.942
b = 91.31	β = 100.364
c = 127.73	γ = 91.113

Software Package:

Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
MoRDa	phasing
Coot	model building

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-06-08 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease, Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	HHSN272201700059C

Revision History  

• Version 1.0: 2022-06-08
  Type: Initial release
  
• Version 1.1: 2023-10-18
  Changes: Data collection, Refinement description