3A8U | pdb_00003a8u

Crystal Structure of omega-Amino Acid:Pyruvate Aminotransferase

• PDB DOI: https://doi.org/10.2210/pdb3A8U/pdb

• Classification: TRANSFERASE
• Organism(s): Pseudomonas putida
• Mutation(s): No 


• Deposited: 2009-10-11 Released: 2009-11-10 
• Deposition Author(s): Watanabe, N., Sakabe, N., Sakabe, K., Sasaki, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 
  0.158 (Depositor), 0.150 (DCC) 
• R-Value Work: 
  0.146 (Depositor), 0.150 (DCC) 
• R-Value Observed: 
  0.147 (Depositor) 

Literature

Crystal Structure of omega-Amino Acid:Pyruvate Aminotransferase

Watanabe, N., Sakabe, N., Sakabe, K., Sasaki, K.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 48.92 kDa 
• Atom Count: 3,774 
• Modeled Residue Count: 441 
• Deposited Residue Count: 449 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Omega-amino acid--pyruvate aminotransferase	A [auth X]	449	Pseudomonas putida	Mutation(s): 0  EC: 2.6.1.18
UniProt
Find proteins for P28269 (Pseudomonas putida) Explore P28269  Go to UniProtKB:  P28269

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PLP	B [auth X]	PYRIDOXAL-5'-PHOSPHATE C8 H10 N O6 P NGVDGCNFYWLIFO-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free:  0.158 (Depositor), 0.150 (DCC) 
• R-Value Work:  0.146 (Depositor), 0.150 (DCC) 
• R-Value Observed: 0.147 (Depositor) 

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 124.46	α = 90
b = 137.79	β = 90
c = 61.57	γ = 90

Software Package:

Software Name	Purpose
BSS	data collection
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-11-10 
Deposition Author(s): Watanabe, N., Sakabe, N., Sakabe, K., Sasaki, K.

Revision History  

• Version 1.0: 2009-11-10
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.2: 2017-10-11
  Changes: Refinement description
• Version 1.3: 2024-03-13
  Changes: Data collection, Database references, Derived calculations