1YXO | pdb_00001yxo

Crystal Structure of pyridoxal phosphate biosynthetic protein PdxA PA0593

• PDB DOI: https://doi.org/10.2210/pdb1YXO/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Pseudomonas aeruginosa
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2005-02-22 Released: 2005-04-05 
• Deposition Author(s): Liu, Y., Xu, X., Dong, A., Kudritskam, M., Savchenko, A., Pai, E.F., Joachimiak, A., Edwards, A., Midwest Center for Structural Genomics (MCSG)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.01 Å
• R-Value Free: 
  0.243 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.198 (Depositor), 0.204 (DCC) 
• R-Value Observed: 
  0.198 (Depositor) 

Literature

Crystal Structure of pyridoxal phosphate biosynthetic protein PdxA PA0593

Liu, Y., Xu, X., Dong, A., Kudritskam, M., Savchenko, A., Pai, E.F., Edwards, A.

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: 71 kDa 
• Atom Count: 5,392 
• Modeled Residue Count: 656 
• Deposited Residue Count: 656 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
4-hydroxythreonine-4-phosphate dehydrogenase 1	A, B	328	Pseudomonas aeruginosa	Mutation(s): 0  Gene Names: pdxA1 EC: 1.1.1.262
UniProt
Find proteins for Q9I5U4 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)) Explore Q9I5U4  Go to UniProtKB:  Q9I5U4

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EOH	E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth B], L [auth B], M [auth B], N [auth B]	ETHANOL C2 H6 O LFQSCWFLJHTTHZ-UHFFFAOYSA-N
MG	C [auth A], D [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

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: 2.01 Å
• R-Value Free:  0.243 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.198 (Depositor), 0.204 (DCC) 
• R-Value Observed: 0.198 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.259	α = 90
b = 59.307	β = 90
c = 199.111	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
SOLVE	phasing
RESOLVE	phasing
ARP/wARP	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-04-05 
Deposition Author(s): Liu, Y., Xu, X., Dong, A., Kudritskam, M., Savchenko, A., Pai, E.F., Joachimiak, A., Edwards, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2005-04-05
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2011-10-05
  Changes: Structure summary
• Version 1.4: 2024-10-30
  Changes: Data collection, Database references, Derived calculations, Structure summary