1YXO

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)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.01 Å
• R-Value Free: 0.243 
• R-Value Work: 0.198 
• R-Value Observed: 0.198 

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 
• Modelled 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 
• R-Value Work: 0.198 
• R-Value Observed: 0.198 
• 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