8YRV

Crystal structure of D-amino acid transaminase from Haliscomenobacter hydrossis complexed with 3-aminooxypropionic acid

• PDB DOI: https://doi.org/10.2210/pdb8YRV/pdb

• Classification: TRANSFERASE
• Organism(s): Haliscomenobacter hydrossis DSM 1100
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-03-21 Released: 2024-04-17 
• Deposition Author(s): Matyuta, I.O., Bakunova, A.K., Nikolaeva, A.Y., Popov, V.O., Boyko, K.M.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.210 
• R-Value Work: 0.166 
• R-Value Observed: 0.168 

Starting Model: experimental

Literature

Crystal structure of D-amino acid transaminase from Haliscomenobacter hydrossis complexed with 3-aminooxypropionic acid

Bakunova, A.K., Matyuta, I.O., Boyko, K.M., Nikolaeva, A.Y., Popov, V.O., Bezsudnova, E.Y.

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)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 32.68 kDa 
• Atom Count: 2,607 
• Modelled Residue Count: 279 
• Deposited Residue Count: 283 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Aminotransferase class IV	A	283	Haliscomenobacter hydrossis DSM 1100	Mutation(s): 0  Gene Names: Halhy_2446
UniProt
Find proteins for F4KWH0 (Haliscomenobacter hydrossis (strain ATCC 27775 / DSM 1100 / LMG 10767 / O)) Explore F4KWH0  Go to UniProtKB:  F4KWH0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
OCF (Subject of Investigation/LOI)	B [auth A]	3-[(~{E})-[2-methyl-3-oxidanyl-5-(phosphonooxymethyl)pyridin-4-yl]methylideneamino]oxypropanoic acid C11 H15 N2 O8 P WFKOVQOIGDESOJ-WLRTZDKTSA-N
MG	C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.210 
• R-Value Work: 0.166 
• R-Value Observed: 0.168 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 86.772	α = 90
b = 71.232	β = 101.26
c = 52.549	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-04-17 
Deposition Author(s): Matyuta, I.O., Bakunova, A.K., Nikolaeva, A.Y., Popov, V.O., Boyko, K.M.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2024-04-17
  Type: Initial release