8ZED | pdb_00008zed

Crystal structure of aldolase AtoB

• PDB DOI: https://doi.org/10.2210/pdb8ZED/pdb

• Classification: BIOSYNTHETIC PROTEIN
• Organism(s): Aspergillus ochraceus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-05-05 Released: 2025-05-14 
• Deposition Author(s): Ma, K., Fan, A., Lin, W.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.37 Å
• R-Value Free: 
  0.321 (Depositor), 0.321 (DCC) 
• R-Value Work: 
  0.260 (Depositor), 0.260 (DCC) 
• R-Value Observed: 
  0.263 (Depositor) 

Starting Model: experimental

Literature

Molecular Basis for the Catalytic Mechanism of the NTF2-like Aldolase in the Biosynthesis of Linear Tetracyclic Meroterpenoids

Ma, K., Fan, A., Lin, W.

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 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 66.82 kDa 
• Atom Count: 4,585 
• Modeled Residue Count: 552 
• Deposited Residue Count: 588 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
AtoB aldolase	A, B, C, D	147	Aspergillus ochraceus	Mutation(s): 0  Gene Names: atoB
UniProt
Find proteins for A0A0U5GHC1 (Aspergillus calidoustus) Explore A0A0U5GHC1  Go to UniProtKB:  A0A0U5GHC1

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	E [auth A], F [auth B], G [auth C], H [auth D]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.37 Å
• R-Value Free:  0.321 (Depositor), 0.321 (DCC) 
• R-Value Work:  0.260 (Depositor), 0.260 (DCC) 
• R-Value Observed: 0.263 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.562	α = 90
b = 122.893	β = 90
c = 69.728	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-05-14 
Deposition Author(s): Ma, K., Fan, A., Lin, W.

---

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	82104056

Revision History  

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