6EFV | pdb_00006efv

The NADPH-dependent sulfite reductase flavoprotein adopts an extended conformation that is unique to this diflavin reductase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.34 Å
  • R-Value Free: 
    0.234 (Depositor), 0.231 (DCC) 
  • R-Value Work: 
    0.167 (Depositor) 
  • R-Value Observed: 
    0.172 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

NADPH-dependent sulfite reductase flavoprotein adopts an extended conformation unique to this diflavin reductase.

Tavolieri, A.M.Murray, D.T.Askenasy, I.Pennington, J.M.McGarry, L.Stanley, C.B.Stroupe, M.E.

(2019) J Struct Biol 205: 170-179

  • DOI: https://doi.org/10.1016/j.jsb.2019.01.001
  • Primary Citation Related Structures: 
    6EFV

  • PubMed Abstract: 

    This is the first X-ray crystal structure of the monomeric form of sulfite reductase (SiR) flavoprotein (SiRFP-60) that shows the relationship between its major domains in an extended position not seen before in any homologous diflavin reductases. Small angle neutron scattering confirms this novel domain orientation also occurs in solution. Activity measurements of SiR and SiRFP variants allow us to propose a novel mechanism for electron transfer from the SiRFP reductase subunit to its oxidase metalloenzyme partner that, together, make up the SiR holoenzyme. Specifically, we propose that SiR performs its 6-electron reduction via intramolecular or intermolecular electron transfer. Our model explains both the significance of the stoichiometric mismatch between reductase and oxidase subunits in the holoenzyme and how SiR can handle such a large volume electron reduction reaction that is at the heart of the sulfur bio-geo cycle.


  • Organizational Affiliation
    • Department of Biological Science and Institute of Molecular Biophysics, 91 Chieftain Way, Tallahassee, FL 32306, USA.

Macromolecule Content 

  • Total Structure Weight: 65.87 kDa 
  • Atom Count: 4,730 
  • Modeled Residue Count: 530 
  • Deposited Residue Count: 569 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Sulfite reductase [NADPH] flavoprotein alpha-component569Escherichia coliMutation(s): 0 
Gene Names: 
EC: 1.8.1.2
UniProt
Find proteins for W8SX42 (Escherichia coli)
Explore W8SX42 
Go to UniProtKB:  W8SX42
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupW8SX42
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FAD

Query on FAD



Download:Ideal Coordinates CCD File
B [auth A]FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
FMN

Query on FMN



Download:Ideal Coordinates CCD File
C [auth A]FLAVIN MONONUCLEOTIDE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
CXS

Query on CXS



Download:Ideal Coordinates CCD File
J [auth A],
K [auth A]
3-CYCLOHEXYL-1-PROPYLSULFONIC ACID
C9 H19 N O3 S
PJWWRFATQTVXHA-UHFFFAOYSA-N
SO4

Query on SO4



Download:Ideal Coordinates CCD File
D [auth A]
E [auth A]
F [auth A]
G [auth A]
H [auth A]
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.34 Å
  • R-Value Free:  0.234 (Depositor), 0.231 (DCC) 
  • R-Value Work:  0.167 (Depositor) 
  • R-Value Observed: 0.172 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 60.483α = 90
b = 99.739β = 90
c = 103.533γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science Foundation (NSF, United States)United StatesMCB1149763

Revision History  (Full details and data files)

  • Version 1.0: 2019-02-27
    Type: Initial release
  • Version 1.1: 2019-11-27
    Changes: Author supporting evidence, Database references
  • Version 1.2: 2023-10-11
    Changes: Data collection, Database references, Refinement description