1PDX

PUTIDAREDOXIN


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 80 
  • Conformers Submitted: 14 
  • Selection Criteria: NO NOE VIOL.>0.5 A, NO DIHEDRAL VIOLATION > 5 DEG. 

wwPDB Validation   3D Report Full Report


This is version 1.5 of the entry. See complete history


Literature

A refined model for the solution structure of oxidized putidaredoxin.

Pochapsky, T.C.Jain, N.U.Kuti, M.Lyons, T.A.Heymont, J.

(1999) Biochemistry 38: 4681-4690

  • DOI: https://doi.org/10.1021/bi983030b
  • Primary Citation of Related Structures:  
    1PDX

  • PubMed Abstract: 

    A refined model for the solution structure of oxidized putidaredoxin (Pdxo), a Cys4Fe2S2 ferredoxin, has been determined. A previous structure (Pochapsky et al. (1994) Biochemistry 33, 6424-6432; PDB entry ) was calculated using the results of homonuclear two-dimensional NMR experiments. New data has made it possible to calculate a refinement of the original Pdxo solution structure. First, essentially complete assignments for diamagnetic 15N and 13C resonances of Pdxo have been made using multidimensional NMR methods, and 15N- and 13C-resolved NOESY experiments have permitted the identification of many new NOE restraints for structural calculations. Stereospecific assignments for leucine and valine CH3 resonances were made using biosynthetically directed fractional 13C labeling, improving the precision of NOE restraints involving these residues. Backbone dihedral angle restraints have been obtained using a combination of two-dimensional J-modulated 15N,1H HSQC and 3D (HN)CO(CO)NH experiments. Second, the solution structure of a diamagnetic form of Pdx, that of the C85S variant of gallium putidaredoxin, in which a nonligand Cys is replaced by Ser, has been determined (Pochapsky et al. (1998) J. Biomol. NMR 12, 407-415), providing information concerning structural features not observable in the native ferredoxin due to paramagnetism. Third, a crystal structure of a closely related ferredoxin, bovine adrenodoxin, has been published (Müller et al. (1998) Structure 6, 269-280). This structure has been used to model the metal binding site structure in Pdx. A family of fourteen structures is presented that exhibits an rmsd of 0.51 A for backbone heavy atoms and 0.83 A for all heavy atoms. Exclusion of the modeled metal binding loop region reduces overall the rmsd to 0.30 A for backbone atoms and 0.71 A for all heavy atoms.


  • Organizational Affiliation

    Departments of Chemistry and Biology, Brandeis University, Waltham, Massachusetts 02254-9110, USA. pochapsky@binah.cc.brandeis.edu


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
PROTEIN (PUTIDAREDOXIN)106Pseudomonas putidaMutation(s): 0 
UniProt
Find proteins for P00259 (Pseudomonas putida)
Explore P00259 
Go to UniProtKB:  P00259
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00259
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FES
Query on FES

Download Ideal Coordinates CCD File 
B [auth A]FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 80 
  • Conformers Submitted: 14 
  • Selection Criteria: NO NOE VIOL.>0.5 A, NO DIHEDRAL VIOLATION > 5 DEG. 

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1999-05-12
    Type: Initial release
  • Version 1.1: 2007-10-16
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-11-29
    Changes: Derived calculations
  • Version 1.4: 2019-11-06
    Changes: Data collection, Database references
  • Version 1.5: 2023-12-27
    Changes: Data collection, Database references, Derived calculations