7BXP | pdb_00007bxp

2-amino-3-ketobutyrate CoA ligase from Cupriavidus necator

PDB DOI: https://doi.org/10.2210/pdb7BXP/pdb

Classification: LIGASE,TRANSFERASE
Organism(s): Cupriavidus necator
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2020-04-20 Released: 2021-04-21
Deposition Author(s): Motoyama, T., Nakano, S., Hasebe, F., Miyoshi, N., Ito, S.
Funding Organization(s): Japan Society for the Promotion of Science (JSPS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free:
0.195 (Depositor), 0.195 (DCC)
R-Value Work:
0.164 (Depositor), 0.165 (DCC)
R-Value Observed:
0.166 (Depositor)

Starting Model: experimental
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This is version 1.2 of the entry. See complete history.

Literature

Chemoenzymatic synthesis of 3-ethyl-2,5-dimethylpyrazine by L-threonine 3-dehydrogenase and 2-amino-3-ketobutyrate CoA ligase/L-threonine aldolase

Motoyama, T., Nakano, S., Hasebe, F., Miyata, R., Kumazawa, S., Miyoshi, N., Ito, S.

(2021) Commun Chem 4: 108-108

DOI: https://doi.org/10.1038/s42004-021-00545-8

Macromolecule Content

Total Structure Weight: 90.16 kDa
Atom Count: 7,000
Modeled Residue Count: 798
Deposited Residue Count: 822
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
2-amino-3-ketobutyrate coenzyme A ligase	A, B	411	Cupriavidus necator	Mutation(s): 0 Gene Names: kbl, H16_B0819 EC: 2.3.1.29
UniProt
Find proteins for Q0K313 (Cupriavidus necator (strain ATCC 17699 / DSM 428 / KCTC 22496 / NCIMB 10442 / H16 / Stanier 337)) Explore Q0K313 Go to UniProtKB: Q0K313
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q0K313
Sequence Annotations Expand
Reference Sequence

Small Molecules

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
LLP Query on LLP	A, B	L-PEPTIDE LINKING	C₁₄ H₂₂ N₃ O₇ P		LYS

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.195 (Depositor), 0.195 (DCC)
R-Value Work: 0.164 (Depositor), 0.165 (DCC)
R-Value Observed: 0.166 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.376	α = 90
b = 105.847	β = 105.791
c = 67.744	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2021-04-21

Deposition Author(s):

Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	18K14391
Japan Society for the Promotion of Science (JSPS)	Japan	19J23697

Revision History (Full details and data files)

Version 1.0: 2021-04-21
Type: Initial release
Version 1.1: 2021-07-28
Changes: Database references
Version 1.2: 2023-11-29
Changes: Data collection, Database references, 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.