8AIE | pdb_00008aie

Crystal structure of D-amino acid aminotransferase from Aminobacterium colombiense complexed with D-cycloserine

• PDB DOI: https://doi.org/10.2210/pdb8AIE/pdb

• Classification: TRANSFERASE
• Organism(s): Aminobacterium colombiense
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2022-07-26 Released: 2022-11-16 
• Deposition Author(s): Matyuta, I.O., Boyko, K.M., Nikolaeva, A.Y., Shilova, S.A., Popov, V.O., Bezsudnova, E.Y.
• Funding Organization(s): Russian Science Foundation

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.264 (Depositor), 0.217 (DCC) 
• R-Value Work: 
  0.219 (Depositor) 
• R-Value Observed: 
  0.221 (Depositor) 

Starting Model: experimental

Literature

3D Structure of D-Аmino Acid Тransaminase from Aminobacterium colombiense in Complex with D-Cycloserine

Shilova, S.A., Matyuta, I.O., Bezsudnova, E.Y., Minyaev, M.E., Nikolaeva, A.Y., Popov, V.O., Boyko, K.M.

(2023) Crystallogr Rep 68: 931-937

• DOI: https://doi.org/10.1134/S1063774523600916

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 63.13 kDa 
• Atom Count: 4,659 
• Modeled Residue Count: 551 
• Deposited Residue Count: 554 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Aminotransferase class IV	A, B	277	Aminobacterium colombiense	Mutation(s): 0  Gene Names: Amico_1844
UniProt
Find proteins for D5EHC5 (Aminobacterium colombiense (strain DSM 12261 / ALA-1)) Explore D5EHC5  Go to UniProtKB:  D5EHC5

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
M7L (Subject of Investigation/LOI)	E [auth B]	3-azanyloxy-2-[(~{E})-[2-methyl-3-oxidanyl-5-(phosphonooxymethyl)pyridin-4-yl]methylideneamino]propanoic acid C11 H16 N3 O8 P ICHYGZXBYNDCFX-NTEUORMPSA-N
LCS (Subject of Investigation/LOI)	C [auth A]	[5-hydroxy-6-methyl-4-({[(4E)-3-oxo-1,2-oxazolidin-4-ylidene]amino}methyl)pyridin-3-yl]methyl dihydrogen phosphate C11 H14 N3 O7 P KFCQHWOGBVCKHR-UKTHLTGXSA-N
PMP (Subject of Investigation/LOI)	D [auth A], F [auth B]	4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE C8 H13 N2 O5 P ZMJGSOSNSPKHNH-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.264 (Depositor), 0.217 (DCC) 
• R-Value Work:  0.219 (Depositor) 
• R-Value Observed: 0.221 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.968	α = 90
b = 90.028	β = 90
c = 100.29	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
CrysalisPro	data reduction
REFMAC	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-11-16 
Deposition Author(s): Matyuta, I.O., Boyko, K.M., Nikolaeva, A.Y., Shilova, S.A., Popov, V.O., Bezsudnova, E.Y.

---

Funding Organization	Location	Grant Number
Russian Science Foundation	Russian Federation	19-14-00164

Revision History  

• Version 1.0: 2022-11-16
  Type: Initial release
  
• Version 1.1: 2024-01-31
  Changes: Data collection, Refinement description
• Version 1.2: 2024-03-06
  Changes: Database references