8ZHU | pdb_00008zhu

Structure of 3-amino-3-carboxyltransferase in complex with 5-thioadenosine in the biosynthesis of nocardicins

PDB DOI: https://doi.org/10.2210/pdb8ZHU/pdb

Classification: TRANSFERASE
Organism(s): Nocardia uniformis subsp. tsuyamanensis
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2024-05-11 Released: 2025-05-14
Deposition Author(s): Gao, Y., Mori, T., Awakawa, T., Abe, I.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free:
0.272 (Depositor), 0.272 (DCC)
R-Value Work:
0.213 (Depositor), 0.215 (DCC)
R-Value Observed:
0.218 (Depositor)

Starting Model: in silico
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Ligand Structure Quality Assessment

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Literature

Structure of 3-amino-3-carboxyltransferase in complex with 5-thioadenosine in the biosynthesis of nocardicins

Gao, Y., Mori, T., Awakawa, T., Abe, I.

To be published.

Macromolecule Content

Total Structure Weight: 71.6 kDa
Atom Count: 4,353
Modeled Residue Count: 571
Deposited Residue Count: 652
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Isonocardicin synthase	A, B	326	Nocardia uniformis subsp. tsuyamanensis	Mutation(s): 0 Gene Names: nat, nocC EC: 2.5.1.38
UniProt
Find proteins for Q9RAH6 (Nocardia uniformis subsp. tsuyamanensis) Explore Q9RAH6 Go to UniProtKB: Q9RAH6
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9RAH6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A4D (Subject of Investigation/LOI) Query on A4D Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth B]	C [auth A], D [auth B]	5'-thioadenosine C₁₀ H₁₃ N₅ O₃ S HLJHWWUZHBUUAC-KQYNXXCUSA-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: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.272 (Depositor), 0.272 (DCC)
R-Value Work: 0.213 (Depositor), 0.215 (DCC)
R-Value Observed: 0.218 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.73	α = 90
b = 94.317	β = 90
c = 136.56	γ = 90

Software Package:

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

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2025-05-14

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2025-05-14
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.