2DAA

CRYSTALLOGRAPHIC STRUCTURE OF D-AMINO ACID AMINOTRANSFERASE INACTIVATED BY D-CYCLOSERINE

• PDB DOI: https://doi.org/10.2210/pdb2DAA/pdb

• Classification: PYRIDOXAL PHOSPHATE
• Organism(s): Bacillus sp. (in: firmicutes)
• Expression System: Saccharomyces cerevisiae
• Mutation(s): No 


• Deposited: 1997-10-27 Released: 1998-03-18 
• Deposition Author(s): Peisach, D., Chipman, D.M., Ringe, D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.260 
• R-Value Work: 0.205 
• R-Value Observed: 0.205 

Starting Model: experimental

Literature

D-Cycloserine Inactivation of D-Amino Acid Aminotransferase Leads to a Stable Noncovalent Protein Complex with an Aromatic Cycloserine-Plp Derivative

Peisach, D., Chipman, D.M., Van Ophem, P.W., Manning, J.M., Petsko, G.A., Ringe, D.

(1998) J Am Chem Soc 120: 2268-2274

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: 65.29 kDa 
• Atom Count: 4,708 
• Modelled Residue Count: 554 
• Deposited Residue Count: 564 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
D-AMINO ACID AMINOTRANSFERASE	A, B	282	Bacillus sp. (in: firmicutes)	Mutation(s): 0  EC: 2.6.1.21
UniProt
Find proteins for P19938 (Bacillus sp. (strain YM-1)) Explore P19938  Go to UniProtKB:  P19938

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DCS	C [auth A], D [auth B]	D-[3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHYL]-N,O-CYCLOSERYLAMIDE C11 H16 N3 O7 P NNRZSZJOQKAGTO-SECBINFHSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.260 
• R-Value Work: 0.205 
• R-Value Observed: 0.205 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.301	α = 90
b = 91.018	β = 90
c = 89.701	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
DENZO	data reduction
SCALEPACK	data scaling
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1998-03-18 
Deposition Author(s): Peisach, D., Chipman, D.M., Ringe, D.

Revision History  

• Version 1.0: 1998-03-18
  Type: Initial release
  
• Version 1.1: 2008-03-24
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-08-09
  Changes: Database references, Derived calculations, Other, Refinement description
• Version 1.4: 2024-05-22
  Changes: Data collection