8ZHV | pdb_00008zhv

Structure of 3-amino-3-carboxyltransferase in complex with SAH and nocardicin G in the biosynthesis of nocardicins

• PDB DOI: https://doi.org/10.2210/pdb8ZHV/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

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.13 Å
• R-Value Free: 
  0.230 (Depositor), 0.225 (DCC) 
• R-Value Work: 
  0.182 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.185 (Depositor) 

Starting Model: in silico

Literature

Structure of 3-amino-3-carboxyltransferase in complex with SAH and nocardicin G in the biosynthesis of nocardicins

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

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 72.47 kDa 
• Atom Count: 4,622 
• Modeled Residue Count: 575 
• Deposited Residue Count: 652 
• Unique protein chains: 1

Macromolecules

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

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1L1U (Subject of Investigation/LOI)	D [auth A], F [auth B]	Nocardicin G C19 H19 N3 O6 SAVAPYNOQXYBJS-JYJNAYRXSA-N
SAH (Subject of Investigation/LOI)	C [auth A]	S-ADENOSYL-L-HOMOCYSTEINE C14 H20 N6 O5 S ZJUKTBDSGOFHSH-WFMPWKQPSA-N
A4D	E [auth B]	5'-thioadenosine C10 H13 N5 O3 S HLJHWWUZHBUUAC-KQYNXXCUSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.13 Å
• R-Value Free:  0.230 (Depositor), 0.225 (DCC) 
• R-Value Work:  0.182 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.185 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.221	α = 90
b = 76.582	β = 90
c = 146.758	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-05-14 
Deposition Author(s): Gao, Y., Mori, T., Awakawa, T., Abe, I.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2025-05-14
  Type: Initial release