4DBE | pdb_00004dbe

Crystal structure of orotidine 5'-monophosphate decarboxylase from Sulfolobus solfataricus complexed with inhibitor BMP

• PDB DOI: https://doi.org/10.2210/pdb4DBE/pdb

• Classification: LYASE/LYASE INHIBITOR
• Organism(s): Saccharolobus solfataricus 98/2
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2012-01-14 Released: 2013-01-16 
• Deposition Author(s): Fedorov, A.A., Fedorov, E.V., Desai, B., Gerlt, J.A., Almo, S.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.79 Å
• R-Value Free: 
  0.236 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.195 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.197 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of orotidine 5'-monophosphate decarboxylase from Sulfolobus solfataricus complexed with inhibitor BMP

Fedorov, A.A., Fedorov, E.V., Desai, B., Gerlt, J.A., Almo, S.C.

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)

Macromolecule Content 

• Total Structure Weight: 50.52 kDa 
• Atom Count: 3,535 
• Modeled Residue Count: 426 
• Deposited Residue Count: 444 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Orotidine 5'-phosphate decarboxylase	A, B	222	Saccharolobus solfataricus 98/2	Mutation(s): 0  Gene Names: pyrF, Ssol_1680 EC: 4.1.1.23
UniProt
Find proteins for D0KT28 (Saccharolobus solfataricus (strain 98/2)) Explore D0KT28  Go to UniProtKB:  D0KT28

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BMP	C [auth A], G [auth B]	6-HYDROXYURIDINE-5'-PHOSPHATE C9 H13 N2 O10 P UDOBICLZEKUKCV-YXZULKJRSA-N
SO4	H [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	D [auth A], E [auth A], F [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.79 Å
• R-Value Free:  0.236 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.195 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.197 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.414	α = 90
b = 41.536	β = 94.08
c = 73.117	γ = 90

Software Package:

Software Name	Purpose
CBASS	data collection
PHENIX	model building
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-01-16 
Deposition Author(s): Fedorov, A.A., Fedorov, E.V., Desai, B., Gerlt, J.A., Almo, S.C.

Revision History  

• Version 1.0: 2013-01-16
  Type: Initial release
  
• Version 1.1: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.2: 2024-11-20
  Changes: Structure summary