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

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free:
0.222 (Depositor), 0.220 (DCC)
R-Value Work:
0.177 (Depositor), 0.180 (DCC)
R-Value Observed:
0.180 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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
Modelled Residue Count: 876
Deposited Residue Count: 932
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

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% Identity50% Identity70% Identity90% Identity95% Identity100% 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), 0.220 (DCC)
R-Value Work: 0.177 (Depositor), 0.180 (DCC)
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

View Full Validation Report

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

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.