8YRU

Crystal structure of D-amino acid transaminase from Haliscomenobacter hydrossis (apo form) after 15 sec of soaking with phenylhydrazine

• PDB DOI: https://doi.org/10.2210/pdb8YRU/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., Minyaev, M.E., Popov, V.O., Boyko, K.M.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.232 
• R-Value Work: 0.177 
• R-Value Observed: 0.179 

Literature

Crystal structure of D-amino acid transaminase from Haliscomenobacter hydrossis (apo form) after 15 sec of soaking with phenylhydrazine

Bakunova, A.K., Matyuta, I.O., Boyko, K.M., Minyaev, M.E., 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: 32.72 kDa 
• Atom Count: 2,321 
• Modelled Residue Count: 271 
• 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
ZXN (Subject of Investigation/LOI)	C [auth A]	[6-methyl-5-oxidanyl-4-[(2-phenylhydrazinyl)methyl]pyridin-3-yl]methyl dihydrogen phosphate C14 H16 N3 O5 P VZZGBIJWEDOPQL-LZYBPNLTSA-N
ACT (Subject of Investigation/LOI)	B [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.232 
• R-Value Work: 0.177 
• R-Value Observed: 0.179 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 87.49	α = 90
b = 71.78	β = 100.72
c = 52.241	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-04-17 
Deposition Author(s): Matyuta, I.O., Bakunova, A.K., Minyaev, M.E., 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