3TFX

Crystal structure of Orotidine 5'-phosphate decarboxylase from Lactobacillus acidophilus

• PDB DOI: https://doi.org/10.2210/pdb3TFX/pdb

• Classification: LYASE
• Organism(s): Lactobacillus acidophilus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2011-08-16 Released: 2011-09-28 
• Deposition Author(s): Satyanarayana, L., Chamala, S., Evans, B., Foti, R., Gizzi, A., Hillerich, B., Kar, A., LaFleur, J., Seidel, R., Villigas, G., Zencheck, W., Almo, S.C., Swaminathan, S., New York Structural Genomics Research Consortium (NYSGRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.19 Å
• R-Value Free: 0.252 
• R-Value Work: 0.205 
• R-Value Observed: 0.207 

Literature

Crystal structure of Orotidine 5'-phosphate decarboxylase from Lactobacillus acidophilus

Satyanarayana, L., Almo, S.C., Swaminathan, S.

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: 57.74 kDa 
• Atom Count: 3,744 
• Modelled Residue Count: 455 
• Deposited Residue Count: 518 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Orotidine 5'-phosphate decarboxylase	A, B	259	Lactobacillus acidophilus	Mutation(s): 0  Gene Names: LBA1386, pyrF, pyrF/LBA1386 EC: 4.1.1.23
UniProt
Find proteins for Q5FJB3 (Lactobacillus acidophilus (strain ATCC 700396 / NCK56 / N2 / NCFM)) Explore Q5FJB3  Go to UniProtKB:  Q5FJB3

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.19 Å
• R-Value Free: 0.252 
• R-Value Work: 0.205 
• R-Value Observed: 0.207 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 130.396	α = 90
b = 68.17	β = 106.31
c = 63.93	γ = 90

Software Package:

Software Name	Purpose
CBASS	data collection
SHELX	model building
REFMAC	refinement
DENZO	data reduction
HKL-2000	data scaling
SHELX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-09-28 
Deposition Author(s): Satyanarayana, L., Chamala, S., Evans, B., Foti, R., Gizzi, A., Hillerich, B., Kar, A., LaFleur, J., Seidel, R., Villigas, G., Zencheck, W., Almo, S.C., Swaminathan, S., New York Structural Genomics Research Consortium (NYSGRC)

Revision History  

• Version 1.0: 2011-09-28
  Type: Initial release