3I94 | pdb_00003i94

Crystal structure of PcyA-biliverdin XIII alpha complex

• PDB DOI: https://doi.org/10.2210/pdb3I94/pdb

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


• Deposited: 2009-07-10 Released: 2009-10-27 
• Deposition Author(s): Hagiwara, Y., Sugishima, M., Fukuyama, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.04 Å
• R-Value Free: 
  0.148 (Depositor), 0.182 (DCC) 
• R-Value Work: 
  0.125 (Depositor), 0.175 (DCC) 
• R-Value Observed: 
  0.125 (Depositor) 

Starting Model: experimental

Literature

Structural insights into vinyl reduction regiospecificity of phycocyanobilin:ferredoxin oxidoreductase (PcyA).

Hagiwara, Y., Sugishima, M., Khawn, H., Kinoshita, H., Inomata, K., Shang, L., Lagarias, J.C., Takahashi, Y., Fukuyama, K.

To be published.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 28.83 kDa 
• Atom Count: 2,535 
• Modeled Residue Count: 243 
• Deposited Residue Count: 248 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phycocyanobilin:ferredoxin oxidoreductase	A	248	Synechocystis sp. PCC 6803	Mutation(s): 0  Gene Names: pcyA, slr0116 EC: 1.3.7.5
UniProt
Find proteins for Q55891 (Synechocystis sp. (strain ATCC 27184 / PCC 6803 / Kazusa)) Explore Q55891  Go to UniProtKB:  Q55891

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BL3	B [auth A]	3-[2-[(Z)-[3-(2-carboxyethyl)-5-[(Z)-(3-ethenyl-4-methyl-5-oxo-pyrrol-2-ylidene)methyl]-4-methyl-pyrrol-2-ylidene]methy l]-5-[(Z)-(3-ethenyl-4-methyl-5-oxo-pyrrol-2-ylidene)methyl]-4-methyl-1H-pyrrol-3-yl]propanoic acid C33 H34 N4 O6 JXYQCWFZZAWTEC-SRVCBVSDSA-N
SO4	C [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.04 Å
• R-Value Free:  0.148 (Depositor), 0.182 (DCC) 
• R-Value Work:  0.125 (Depositor), 0.175 (DCC) 
• R-Value Observed: 0.125 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.785	α = 90
b = 94.797	β = 90
c = 42.653	γ = 90

Software Package:

Software Name	Purpose
SHELX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
SCALEPACK	data scaling
SHELXL	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-10-27 
Deposition Author(s): Hagiwara, Y., Sugishima, M., Fukuyama, K.

Revision History  

• Version 1.0: 2009-10-27
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary