Biological Assembly 1  

 3D View: Structure | 1D-3D View | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content

• Total Structure Weight: 28.76 kDa 
• Atom Count: 2252 
• Modelled Residue Count: 242 
• Deposited Residue Count: 248 
• Unique protein chains: 1

4QCD

Neutron crystal structure of phycocyanobilin:ferredoxin oxidoreductase in complex with biliverdin IXalpha at room temperature.

• PDB DOI: 10.2210/pdb4QCD/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Synechocystis sp. PCC 6803 substr. Kazusa
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2014-05-10 Released: 2015-04-29 
• Deposition Author(s): Unno, M., Ishikawa-Suto, K., Ishihara, M., Hagiwara, Y., Sugishima, M., Wada, K., Fukuyama, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free: 0.165 
• R-Value Work: 0.143 
• R-Value Observed: 0.145 

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• Method: NEUTRON DIFFRACTION
• Resolution: 1.93 Å
• R-Value Free: 0.227 
• R-Value Work: 0.167 
• R-Value Observed: 0.173 

Literature

Insights into the Proton Transfer Mechanism of a Bilin Reductase PcyA Following Neutron Crystallography.

Unno, M., Ishikawa-Suto, K., Kusaka, K., Tamada, T., Hagiwara, Y., Sugishima, M., Wada, K., Yamada, T., Tomoyori, K., Hosoya, T., Tanaka, I., Niimura, N., Kuroki, R., Inaka, K., Ishihara, M., Fukuyama, K.

(2015) J Am Chem Soc 137: 5452-5460

• PubMed: 25872660 
• DOI: 10.1021/jacs.5b00645
• Primary Citation of Related Structures:  
  4QCD


• PubMed Abstract: 
  

Phycocyanobilin, a light-harvesting and photoreceptor pigment in higher plants, algae, and cyanobacteria, is synthesized from biliverdin IXα (BV) by phycocyanobilin:ferredoxin oxidoreductase (PcyA) via two steps of two-proton-coupled two-electron reduction. We determined the neutron structure of PcyA from cyanobacteria complexed with BV, revealing the exact location of the hydrogen atoms involved in catalysis. Notably, approximately half of the BV bound to PcyA was BVH(+), a state in which all four pyrrole nitrogen atoms were protonated. The protonation states of BV complemented the protonation of adjacent Asp105. The "axial" water molecule that interacts with the neutral pyrrole nitrogen of the A-ring was identified. His88 Nδ was protonated to form a hydrogen bond with the lactam O atom of the BV A-ring. His88 and His74 were linked by hydrogen bonds via H3O(+). These results imply that Asp105, His88, and the axial water molecule contribute to proton transfer during PcyA catalysis.

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Organizational Affiliation: 

◆Graduate School of Engineering, Osaka University, Suita 565-0871, Japan.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phycocyanobilin:ferredoxin oxidoreductase	A	248	Synechocystis sp. PCC 6803 substr. Kazusa	Mutation(s): 0  Gene Names: pcyA, slr0116 EC: 1.3.7.5
UniProt
Find proteins for Q55891 (Synechocystis sp. (strain PCC 6803 / Kazusa)) Explore Q55891  Go to UniProtKB:  Q55891

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BLA	B [auth A]	BILIVERDINE IX ALPHA C33 H34 N4 O6 GWZYPXHJIZCRAJ-SRVCBVSDSA-N
D3O	C [auth A]	trideuteriooxidanium D3 O XLYOFNOQVPJJNP-ZRLBSURWSA-O

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free: 0.165 
• R-Value Work: 0.143 
• R-Value Observed: 0.145 
• Space Group: P 2₁ 2₁ 2

• Method: NEUTRON DIFFRACTION
• Resolution: 1.93 Å
• R-Value Free: 0.227 
• R-Value Work: 0.167 
• R-Value Observed: 0.173 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.107	α = 90
b = 97.278	β = 90
c = 43.174	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
CNS	refinement
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2014-05-10 
• Released Date: 2015-04-29 
Deposition Author(s): Unno, M., Ishikawa-Suto, K., Ishihara, M., Hagiwara, Y., Sugishima, M., Wada, K., Fukuyama, K.

Revision History  

• Version 1.0: 2015-04-29
  Type: Initial release
  
• Version 1.1: 2018-01-24
  Changes: Experimental preparation
• Version 1.2: 2018-04-04
  Changes: Data collection, Database references
• Version 2.0: 2021-06-09
  Changes: Derived calculations, Non-polymer description