4DBD | pdb_00004dbd

Crystal structure of orotidine 5'-monophosphate decarboxylase from Sulfolobus solfataricus

• PDB DOI: https://doi.org/10.2210/pdb4DBD/pdb

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


• Deposited: 2012-01-14 Released: 2013-02-13 
• 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: 1.70 Å
• R-Value Free: 
  0.245 (Depositor), 0.242 (DCC) 
• R-Value Work: 
  0.208 (Depositor), 0.207 (DCC) 
• R-Value Observed: 
  0.210 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of orotidine 5'-monophosphate decarboxylase from Sulfolobus solfataricus

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: 25.02 kDa 
• Atom Count: 1,750 
• Modeled Residue Count: 210 
• Deposited Residue Count: 222 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Orotidine 5'-phosphate decarboxylase	A	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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	B [auth A], C [auth A], D [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.245 (Depositor), 0.242 (DCC) 
• R-Value Work:  0.208 (Depositor), 0.207 (DCC) 
• R-Value Observed: 0.210 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 40.367	α = 90
b = 64.819	β = 90
c = 73.237	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: 2013-02-13 
Deposition Author(s): Fedorov, A.A., Fedorov, E.V., Desai, B., Gerlt, J.A., Almo, S.C.

Revision History  

• Version 1.0: 2013-02-13
  Type: Initial release
  
• Version 1.1: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description