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)

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
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Ligand Structure Quality Assessment

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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.

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

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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 Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A0A1EQY0
Sequence Annotations Expand
Reference Sequence

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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	3D Interactions
CYC (Subject of Investigation/LOI) Query on CYC Download:Ideal Coordinates CCD File SDF format, chain E [auth F] SDF format, chain F [auth C] MOL2 format, chain E [auth F] MOL2 format, chain F [auth C] mmCIF format, chain E [auth F] mmCIF format, chain F [auth C]	E [auth F], F [auth C]	PHYCOCYANOBILIN C₃₃ H₄₀ N₄ O₆ VXTXPYZGDQPMHK-GMXXPEQVSA-N		Interactions Focus chain E [auth F] Focus chain F [auth C] Interactions & Density Focus chain E [auth F] Focus chain F [auth C]

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

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Entry History

& Funding Information

Deposition Data

Released Date: 2025-11-05

Deposition Author(s):

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 (Full details and data files)

Version 1.0: 2025-11-05
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.