6LK1

Ultrahigh resolution X-ray structure of Ferredoxin I from C. reinhardtii


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.90 Å
  • R-Value Free: 0.171 
  • R-Value Work: 0.145 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

X-ray dose-dependent structural changes of the [2Fe-2S] ferredoxin from Chlamydomonas reinhardtii.

Ohnishi, Y.Muraki, N.Kiyota, D.Okumura, H.Baba, S.Kawano, Y.Kumasaka, T.Tanaka, H.Kurisu, G.

(2020) J Biochem 167: 549-555

  • DOI: 10.1093/jb/mvaa045
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Plant-type ferredoxin (Fd) is an electron transfer protein in chloroplast. Redox-dependent structural change of Fd controls its association with and dissociation from Fd-dependent enzymes. Among many X-ray structures of oxidized Fd have been reported ...

    Plant-type ferredoxin (Fd) is an electron transfer protein in chloroplast. Redox-dependent structural change of Fd controls its association with and dissociation from Fd-dependent enzymes. Among many X-ray structures of oxidized Fd have been reported so far, very likely a given number of them was partially reduced by strong X-ray. To understand the precise structural change between reduced and oxidized Fd, it is important to know whether the crystals of oxidized Fd may or may not be reduced during the X-ray experiment. We prepared the thin plate-shaped Fd crystals from Chlamydomonas reinhardtii and monitored its absorption spectra during experiment. Absorption spectra of oxidized Fd crystals were clearly changed to that of reduced form in an X-ray dose-dependent manner. In another independent experiment, the X-ray diffraction images obtained from different parts of one single crystal were sorted and merged to form two datasets with low and high X-ray doses. An Fo-Fo map calculated from the two datasets showed that X-ray reduction causes a small displacement of the iron atoms in the [2Fe-2S] cluster. Both our spectroscopic and crystallographic studies confirm X-ray dose-dependent reduction of Fd, and suggest a structural basis for its initial reduction step especially in the core of the cluster.


    Organizational Affiliation

    Department of Macromolecular Science, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka, Japan.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ferredoxin, chloroplastic
A, B
95Chlamydomonas reinhardtiiMutation(s): 0 
Gene Names: PETF
Find proteins for P07839 (Chlamydomonas reinhardtii)
Go to UniProtKB:  P07839
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FES
Query on FES

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A, B
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
 Ligand Interaction
BEN
Query on BEN

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A, B
BENZAMIDINE
C7 H8 N2
PXXJHWLDUBFPOL-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

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A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
SCN
Query on SCN

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A
THIOCYANATE ION
C N S
ZMZDMBWJUHKJPS-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.90 Å
  • R-Value Free: 0.171 
  • R-Value Work: 0.145 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 25.955α = 90
b = 60.09β = 102.4
c = 50.085γ = 90
Software Package:
Software NamePurpose
SHELXrefinement
PDB_EXTRACTdata extraction
MOSFLMdata reduction
Aimlessdata scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Education, Culture, Sports, Science and Technology (Japan)Japan--

Revision History 

  • Version 1.0: 2020-05-27
    Type: Initial release
  • Version 1.1: 2020-06-10
    Changes: Database references