3WCQ | pdb_00003wcq

Crystal structure analysis of Cyanidioschyzon melorae ferredoxin D58N mutant

• PDB DOI: https://doi.org/10.2210/pdb3WCQ/pdb

• Classification: ELECTRON TRANSPORT
• Organism(s): Cyanidioschyzon merolae
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2013-05-31 Released: 2013-08-07 
• Deposition Author(s): Ueno, Y., Matsumoto, T., Yamano, A., Imai, T., Morimoto, Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 0.97 Å
• R-Value Free: 
  0.170 (Depositor), 0.174 (DCC) 
• R-Value Work: 
  0.151 (Depositor) 
• R-Value Observed: 
  0.152 (Depositor) 

Literature

Increasing the electron-transfer ability of Cyanidioschyzon merolae ferredoxin by a one-point mutation - A high resolution and Fe-SAD phasing crystal structure analysis of the Asp58Asn mutant

Ueno, Y., Matsumoto, T., Yamano, A., Imai, T., Morimoto, Y.

(2013) Biochem Biophys Res Commun 436: 736-739

• PubMed: 23792094 
• DOI: https://doi.org/10.1016/j.bbrc.2013.06.029
• Primary Citation Related Structures: 
  3WCQ


• PubMed Abstract: 
  

  Cyanidioschyzon merolae (Cm) is a single cell red algae that grows in rather thermophilic (40-50°C) and acidic (pH 1-3) conditions. Ferredoxin (Fd) was purified from this algae and characterized as a plant-type [2Fe-2S] Fd by physicochemical techniques. A high resolution (0.97Å) three-dimensional structure of the CmFd D58N mutant molecule has been determined using the Fe-SAD phasing method to clarify the precise position of the Asn58 amide, as this substitution increases the electron-transfer ability relative to wild-type CmFd by a factor of 1.5. The crystal structure reveals an electro-positive surface surrounding Asn58 that may interact with ferredoxin NADP(+) reductase or cytochrome c.

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Organizational Affiliation: 
• Department of Life Science and Graduate School of Life Science, Rikkyo (St. Paul's ) University, Toshima-ku, Tokyo 171-8501, Japan.

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: 10.76 kDa 
• Atom Count: 828 
• Modeled Residue Count: 97 
• Deposited Residue Count: 97 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ferredoxin	A	97	Cyanidioschyzon merolae	Mutation(s): 1  Gene Names: petF
UniProt
Find proteins for Q85FT5 (Cyanidioschyzon merolae (strain NIES-3377 / 10D)) Explore Q85FT5  Go to UniProtKB:  Q85FT5

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FES	B [auth A]	FE2/S2 (INORGANIC) CLUSTER Fe2 S2 NIXDOXVAJZFRNF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 0.97 Å
• R-Value Free:  0.170 (Depositor), 0.174 (DCC) 
• R-Value Work:  0.151 (Depositor) 
• R-Value Observed: 0.152 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 34.026	α = 90
b = 46.527	β = 90
c = 66.139	γ = 90

Software Package:

Software Name	Purpose
CrystalClear	data collection
CRANK	phasing
REFMAC	refinement
CrystalClear	data reduction
CrystalClear	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-08-07 
Deposition Author(s): Ueno, Y., Matsumoto, T., Yamano, A., Imai, T., Morimoto, Y.

Revision History  

• Version 1.0: 2013-08-07
  Type: Initial release
  
• Version 1.1: 2024-03-20
  Changes: Data collection, Database references, Derived calculations