6ZHK | pdb_00006zhk

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

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free:
0.222 (Depositor), 0.229 (DCC)
R-Value Work:
0.177 (Depositor)
R-Value Observed:
0.180 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.3 of the entry. See complete history.

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

Macromolecule Content

Total Structure Weight: 105.98 kDa
Atom Count: 7,407
Modeled Residue Count: 876
Deposited Residue Count: 932
Unique protein chains: 1

Macromolecules

Find similar proteins by:

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q58696
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth B] SDF format, chain E [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B] MOL2 format, chain E [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth B] mmCIF format, chain E [auth B]	C [auth A], D [auth B], E [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Focus chain E [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B] Focus chain E [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.222 (Depositor), 0.229 (DCC)
R-Value Work: 0.177 (Depositor)
R-Value Observed: 0.180 (Depositor)

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

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Entry History

& Funding Information

Deposition Data

Released Date: 2020-07-01

Deposition Author(s):

Nikolaeva, T.N.

Stekhanova, T.N.

Bezsudnova, E.Y.

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

Revision History (Full details and data files)

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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.