9KA8 | pdb_00009ka8

Structure of the recombinant structure of the subunit of allophycocyanin (APC) and the formate dehydrogenase (FDH)

• PDB DOI: https://doi.org/10.2210/pdb9KA8/pdb

• Classification: PHOTOSYNTHESIS
• Organism(s): [Candida] boidinii, Picosynechococcus sp. PCC 7003
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-10-28 Released: 2025-11-05 
• Deposition Author(s): Duan, M.P., Zhang, T.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.19 Å
• R-Value Free: 
  0.217 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.188 (Depositor), 0.189 (DCC) 
• R-Value Observed: 
  0.189 (Depositor) 

Starting Models: experimental

Literature

Structure of the recombinant structure of the subunit of allophycocyanin (APC) and the formate dehydrogenase (FDH)

Duan, M.P., Zhang, T.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 114.14 kDa 
• Atom Count: 8,852 
• Modeled Residue Count: 997 
• Deposited Residue Count: 1,030 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Formate dehydrogenase	A [auth B], C [auth A]	355	[Candida] boidinii	Mutation(s): 0  Gene Names: FDH, Cboi02_000553900 EC: 1.17.1.9
UniProt
Find proteins for A0A0A1EQY0 (Candida boidinii) Explore A0A0A1EQY0  Go to UniProtKB:  A0A0A1EQY0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Allophycocyanin	B [auth F], D [auth C]	160	Picosynechococcus sp. PCC 7003	Mutation(s): 0  Gene Names: AWQ21_08925

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CYC (Subject of Investigation/LOI)	E [auth F], F [auth C]	PHYCOCYANOBILIN C33 H40 N4 O6 VXTXPYZGDQPMHK-GMXXPEQVSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.19 Å
• R-Value Free:  0.217 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.188 (Depositor), 0.189 (DCC) 
• R-Value Observed: 0.189 (Depositor) 

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 189.784	α = 90
b = 189.784	β = 90
c = 153.879	γ = 120

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-11-05 
Deposition Author(s): Duan, M.P., Zhang, T.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	32472277
National Natural Science Foundation of China (NSFC)	China	32372320

Revision History  

• Version 1.0: 2025-11-05
  Type: Initial release