7P8O

Crystal structure of D-aminoacid transaminase from Haliscomenobacter hydrossis in its intermediate form

• PDB DOI: https://doi.org/10.2210/pdb7P8O/pdb

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


• Deposited: 2021-07-23 Released: 2022-08-03 
• Deposition Author(s): Matyuta, I.O., Boyko, K.M., Bakunova, A.K., Nikolaeva, A.Y., Rakitina, T.V., Bezsudnova, E.Y., Popov, V.O.
• Funding Organization(s): Russian Science Foundation

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.232 
• R-Value Work: 0.191 
• R-Value Observed: 0.193 

Starting Model: experimental

Literature

Crystal structure of D-aminoacid transaminase from Haliscomenobacter hydrossis in its apo form

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

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: 32.44 kDa 
• Atom Count: 2,261 
• Modelled Residue Count: 275 
• 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
SO4	B [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
MG	C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.232 
• R-Value Work: 0.191 
• R-Value Observed: 0.193 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 87.636	α = 90
b = 72.374	β = 100.05
c = 51.822	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-08-03 
Deposition Author(s): Matyuta, I.O., Boyko, K.M., Bakunova, A.K., Nikolaeva, A.Y., Rakitina, T.V., Bezsudnova, E.Y., Popov, V.O.

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

Revision History  

• Version 1.0: 2022-08-03
  
• Version 1.1: 2024-01-31
  
• Version 2.0: 2024-07-03
  Type: Coordinate replacement
  Reason: Atoms with unrealistic or zero occupancies
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Refinement description, Source and taxonomy, Structure summary