5H8V

Crystal structure of the complex between maize Sulfite Reductase and ferredoxin in the form-1 crystal


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.200 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural and mutational studies of an electron transfer complex of maize sulfite reductase and ferredoxin.

Kim, J.Y.Nakayama, M.Toyota, H.Kurisu, G.Hase, T.

(2016) J.Biochem. 160: 101-109

  • DOI: 10.1093/jb/mvw016
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The structure of the complex of maize sulfite reductase (SiR) and ferredoxin (Fd) has been determined by X-ray crystallography. Co-crystals of the two proteins prepared under different conditions were subjected to the diffraction analysis and three p ...

    The structure of the complex of maize sulfite reductase (SiR) and ferredoxin (Fd) has been determined by X-ray crystallography. Co-crystals of the two proteins prepared under different conditions were subjected to the diffraction analysis and three possible structures of the complex were solved. Although topological relationship of SiR and Fd varied in each of the structures, two characteristics common to all structures were found in the pattern of protein-protein interactions and positional arrangements of redox centres; (i) a few negative residues of Fd contact with a narrow area of SiR with positive electrostatic surface potential and (ii) [2Fe-2S] cluster of Fd and [4Fe-4S] cluster of SiR are in a close proximity with the shortest distance around 12 Å. Mutational analysis of a total of seven basic residues of SiR distributed widely at the interface of the complex showed their importance for supporting an efficient Fd-dependent activity and a strong physical binding to Fd. These combined results suggest that the productive electron transfer complex of SiR and Fd could be formed through multiple processes of the electrostatic intermolecular interaction and this implication is discussed in terms of the multi-functionality of Fd in various redox metabolisms.


    Organizational Affiliation

    Division of Protein Structural Biology, Institute for Protein Research, Osaka University, Yamadaoka 3-2, Suita, Osaka 565-0871, Japan gkurisu@protein.osaka-u.ac.jp.,Division of Protein Chemistry and.,Division of Protein Chemistry and enzyme@protein.osaka-u.ac.jp.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Sulfite reductase [ferredoxin], chloroplastic
A, B
583Zea maysMutation(s): 0 
Gene Names: SIR
EC: 1.8.7.1
Find proteins for O23813 (Zea mays)
Go to UniProtKB:  O23813
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SF4
Query on SF4

Download SDF File 
Download CCD File 
A, B
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
PO4
Query on PO4

Download SDF File 
Download CCD File 
A, B
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
SRM
Query on SRM

Download SDF File 
Download CCD File 
A, B
SIROHEME
C42 H42 Fe N4 O16
PGYXHNRRBJLFEV-NBUGCWMUSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.200 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 103.346α = 90.00
b = 103.346β = 90.00
c = 255.048γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
SHARPphasing
REFMACrefinement
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Science and Technology AgencyJapanCREST
Cabinet office of JapanJapanGS016

Revision History 

  • Version 1.0: 2016-04-13
    Type: Initial release
  • Version 1.1: 2016-08-10
    Type: Database references