6ZHK

Crystal structure of adenosylmethionine-8-amino-7-oxononanoate aminotransferase from Methanocaldococcus jannaschii DSM 2661

• PDB DOI: https://doi.org/10.2210/pdb6ZHK/pdb

• Classification: TRANSFERASE
• Organism(s): Methanocaldococcus jannaschii DSM 2661
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2020-06-23 Released: 2020-07-01 
• Deposition Author(s): Boyko, K.M., Nikolaeva, T.N., Stekhanova, T.N., 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: 1.80 Å
• R-Value Free: 0.222 
• R-Value Work: 0.177 
• R-Value Observed: 0.180 

Literature

Three-Dimensional Structure of Thermostable D-Amino Acid Transaminase from the Archaeon Methanocaldococcus jannaschii DSM 2661

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

(2021) Crystallogr Rep 

• DOI: https://doi.org/10.1134/S1063774521050035

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: 105.98 kDa 
• Atom Count: 7,407 
• Modelled Residue Count: 876 
• Deposited Residue Count: 932 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Adenosylmethionine-8-amino-7-oxononanoate aminotransferase	A, B	466	Methanocaldococcus jannaschii DSM 2661	Mutation(s): 3  Gene Names: bioA, MJ1300 EC: 2.6.1.62
UniProt
Find proteins for Q58696 (Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440)) Explore Q58696  Go to UniProtKB:  Q58696

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MG	C [auth A], D [auth B], E [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.222 
• R-Value Work: 0.177 
• R-Value Observed: 0.180 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.232	α = 106.11
b = 61.38	β = 93.48
c = 63.069	γ = 96.47

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-07-01 
Deposition Author(s): Boyko, K.M., Nikolaeva, T.N., Stekhanova, T.N., 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: 2020-07-01
  Type: Initial release
  
• Version 1.1: 2020-07-08
  Changes: Database references
• Version 1.2: 2022-01-19
  Changes: Database references, Derived calculations
• Version 1.3: 2024-01-24
  Changes: Data collection, Refinement description