8ZXB | pdb_00008zxb

Structure of aminotransferase from Mycolicibacterium neoaurum in complex with PLP

PDB DOI: https://doi.org/10.2210/pdb8ZXB/pdb

Classification: TRANSFERASE
Organism(s): Mycolicibacterium neoaurum
Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
Mutation(s): No

Deposited: 2024-06-14 Released: 2025-06-18
Deposition Author(s): Wei, H., Cong, L., Wang, J., You, S., Liu, W.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.75 Å
R-Value Free:
0.203 (Depositor), 0.206 (DCC)
R-Value Work:
0.171 (Depositor), 0.175 (DCC)
R-Value Observed:
0.172 (Depositor)

Starting Model: in silico
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Ligand Structure Quality Assessment

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Literature

Structure of aminotransferase from Mycolicibacterium neoaurum in complex with PLP

Wei, H., Cong, L., Wang, J., You, S., Liu, W.

To be published.

Macromolecule Content

Total Structure Weight: 143.83 kDa
Atom Count: 10,972
Modeled Residue Count: 1,236
Deposited Residue Count: 1,304
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Branched-chain amino acid aminotransferase	A, B, C, D	326	Mycolicibacterium neoaurum	Mutation(s): 0 Gene Names: SAMN04488581_1910
UniProt
Find proteins for A0AAV2WF13 (Mycolicibacterium neoaurum) Explore A0AAV2WF13 Go to UniProtKB: A0AAV2WF13
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0AAV2WF13
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PLP (Subject of Investigation/LOI) Query on PLP Download:Ideal Coordinates CCD File SDF format, chain H [auth D] SDF format, chain G [auth C] SDF format, chain F [auth B] SDF format, chain E [auth A] MOL2 format, chain H [auth D] MOL2 format, chain G [auth C] MOL2 format, chain F [auth B] MOL2 format, chain E [auth A] mmCIF format, chain H [auth D] mmCIF format, chain G [auth C] mmCIF format, chain F [auth B] mmCIF format, chain E [auth A]	E [auth A], F [auth B], G [auth C], H [auth D]	PYRIDOXAL-5'-PHOSPHATE C₈ H₁₀ N O₆ P NGVDGCNFYWLIFO-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth C] Focus chain H [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth C] Focus chain H [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.75 Å
R-Value Free: 0.203 (Depositor), 0.206 (DCC)
R-Value Work: 0.171 (Depositor), 0.175 (DCC)
R-Value Observed: 0.172 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.08	α = 96.92
b = 79.08	β = 108.47
c = 91.98	γ = 113.09

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
XDS	data reduction
PHASER	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2025-06-18

Deposition Author(s):

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	--

Revision History (Full details and data files)

Version 1.0: 2025-06-18
Type: Initial release

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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.