5LJP

E20K/I59A/E72K/I92A/D126K/A142V FLAVODOXIN FROM ANABAENA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.1 Å
  • R-Value Free: 0.176 
  • R-Value Work: 0.160 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Direct examination of the relevance for folding, binding and electron transfer of a conserved protein folding intermediate.

Lamazares, E.Vega, S.Ferreira, P.Medina, M.Galano-Frutos, J.J.Martinez-Julvez, M.Velazquez-Campoy, A.Sancho, J.

(2017) Phys Chem Chem Phys 19: 19021-19031

  • DOI: 10.1039/c7cp02606d

  • PubMed Abstract: 
  • Near the minimum free energy basin of proteins where the native ensemble resides, partly unfolded conformations of slightly higher energy can be significantly populated under native conditions. It has been speculated that they play roles in molecular ...

    Near the minimum free energy basin of proteins where the native ensemble resides, partly unfolded conformations of slightly higher energy can be significantly populated under native conditions. It has been speculated that they play roles in molecular recognition and catalysis, but they might represent contemporary features of the evolutionary process without functional relevance. Obtaining conclusive evidence on these alternatives is difficult because it requires comparing the performance of a given protein when populating and when not populating one such intermediate, in otherwise identical conditions. Wild type apoflavodoxin populates under native conditions a partly unfolded conformation (10% of molecules) whose unstructured region includes the binding sites for the FMN cofactor and for redox partner proteins. We recently engineered a thermostable variant where the intermediate is no longer detectable. Using the wild type and variant, we assess the relevance of the intermediate comparing folding kinetics, cofactor binding kinetics, cofactor affinity, X-ray structure, intrinsic dynamics, redox potential of the apoflavodoxin-cofactor complex (Fld), its affinity for partner protein FNR, and electron transfer rate within the Fld/FNR physiological complex. Our data strongly suggest the intermediate state, conserved in long-chain apoflavodoxins, is not required for the correct assembly of flavodoxin nor does it contribute to shape its electron transfer properties. This analysis can be applied to evaluate other native basin intermediates.


    Organizational Affiliation

    Biocomputation and Complex Systems Physics Institute (BIFI)-Joint Units: BIFI-IQFR (CSIC) and GBsC-CSIC, Universidad de Zaragoza, Zaragoza, Spain and Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, Zaragoza, Spain.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Flavodoxin
A
169Nostoc sp. (strain ATCC 29151 / PCC 7119)Mutation(s): 6 
Gene Names: isiB
Find proteins for P0A3E0 (Nostoc sp. (strain ATCC 29151 / PCC 7119))
Go to UniProtKB:  P0A3E0
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FMN
Query on FMN

Download SDF File 
Download CCD File 
A
FLAVIN MONONUCLEOTIDE
RIBOFLAVIN MONOPHOSPHATE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
FMNKa: 83000000 M-1 BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.1 Å
  • R-Value Free: 0.176 
  • R-Value Work: 0.160 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 37.919α = 90.00
b = 62.911β = 90.00
c = 64.650γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
ALBA synchrotronSpain2012010062

Revision History 

  • Version 1.0: 2017-08-02
    Type: Initial release