8ZPI | pdb_00008zpi

The cryoEM structure of a daminobutyrate--2-oxoglutarate transaminase EctB

PDB DOI: https://doi.org/10.2210/pdb8ZPI/pdb
EM Map EMD-60345: EMDB EMDataResource

Classification: TRANSFERASE
Organism(s): Parageobacillus caldoxylosilyticus
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2024-05-30 Released: 2025-06-04
Deposition Author(s): Jiang, W.X., Cheng, X.Q., Ma, L.X., Xing, Q.
Funding Organization(s): National Basic Research Program of China (973 Program)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.12 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

Validation slider image for 8ZPI

This is version 1.0 of the entry. See complete history.

Literature

The cryoEM structure of a daminobutyrate--2-oxoglutarate transaminase EctB

Jiang, W.X., Cheng, X.Q., Ma, L.X., Xing, Q.

To be published.

Macromolecule Content

Total Structure Weight: 108.93 kDa
Atom Count: 7,649
Modeled Residue Count: 962
Deposited Residue Count: 962
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Diaminobutyrate-2-oxoglutarate transaminase	A, B	481	Parageobacillus caldoxylosilyticus	Mutation(s): 0 Gene Names: B4119_1990 EC: 2.6.1.76
UniProt
Find proteins for A0A150LFB8 (Saccharococcus caldoxylosilyticus) Explore A0A150LFB8 Go to UniProtKB: A0A150LFB8
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A150LFB8
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 D [auth B] SDF format, chain C [auth A] MOL2 format, chain D [auth B] MOL2 format, chain C [auth A] mmCIF format, chain D [auth B] mmCIF format, chain C [auth A]	C [auth A], D [auth B]	PYRIDOXAL-5'-PHOSPHATE C₈ H₁₀ N O₆ P NGVDGCNFYWLIFO-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.12 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Structure Validation

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2025-06-04

Deposition Author(s):

Funding Organization	Location	Grant Number
National Basic Research Program of China (973 Program)	China	2021YFC2100100

Revision History (Full details and data files)

Version 1.0: 2025-06-04
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.