1GPX

C85S GAPDX, NMR, 20 STRUCTURES


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 20 
  • Selection Criteria: LEAST RESTRAINT VIOLATION 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

The solution structure of a gallium-substituted putidaredoxin mutant: GaPdx C85S.

Pochapsky, T.C.Kuti, M.Kazanis, S.

(1998) J.Biomol.NMR 12: 407-415


  • PubMed Abstract: 
  • The Fe2S2 cluster of the ferredoxin putidaredoxin (Pdx) can be replaced by a single gallium ion, giving rise to a colorless, diamagnetic protein in which, apart from the metal binding site, the major structural features of the native ferredoxin are c ...

    The Fe2S2 cluster of the ferredoxin putidaredoxin (Pdx) can be replaced by a single gallium ion, giving rise to a colorless, diamagnetic protein in which, apart from the metal binding site, the major structural features of the native ferredoxin are conserved. The solution structure of the C85S variant of gallium putidaredoxin (C85S GaPdx), in which a non-ligand cysteine is replaced by a serine, has been determined via multidimensional NMR methods using uniformly 15N, 13C labeled samples of C85S GaPdx. Stereospecific assignments of leucine and valine methyl resonances were made using 13C, 1H HSQC spectra obtained with fractionally 13C-labeled samples, and backbone dihedral angle restraints were obtained using a combination of two-dimensional J-modulated 15N, 1H HSQC and three-dimensional (HN)CO(CO)NH experiments. A total of 1117 NOE-derived distance restraints were used in the calculations, including 454 short range (i-j < or = 3), 456 long range (i-j > or = 4) interresidue restraints and 207 non-trivial intraresidue restraints. 97 phi and 55 chi 1 angular restraints were also included in the calculation of a family of 20 structures using a combined distance geometry-simulated annealing protocol. Most regions of the protein are well defined in the calculations, with an RMSD of 0.525 A for backbone atoms excluding the metal binding loop (residues 34-48) and the last three C-terminal residues (residues 103-106). Where comparison is possible, these regions show an increase in dynamic behavior over the native protein, as does the loop containing residues 74-76. Structural and dynamic differences between native Pdx and GaPdx are discussed in relation to charge and packing of the metal binding site.


    Related Citations: 
    • Structural Features of the Metal Binding Site and Dynamics of Gallium Putidaredoxin, a Diamagnetic Derivative of a Cys4Fe2S2 Ferredoxin
      Kazanis, S.,Pochapsky, T.C.
      (1997) J.Biomol.NMR 9: 337
    • Conversion of a Fe2S2 Ferredoxin Into a Ga+3 Rubredoxin
      Kazanis, S.,Pochapsky, T.C.,Barnhart, T.M.,Penner-Hahn, J.E.,Mirza, U.A.,Chait, B.T.
      (1995) J.Am.Chem.Soc. 117: 6625


    Organizational Affiliation

    Department of Chemistry, Brandeis University, Waltham, MA 02254-9110, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PUTIDAREDOXIN
A
106Pseudomonas putidaGene Names: camB
Find proteins for P00259 (Pseudomonas putida)
Go to UniProtKB:  P00259
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GA
Query on GA

Download SDF File 
Download CCD File 
A
GALLIUM (III) ION
Ga
CKHJYUSOUQDYEN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 20 
  • Selection Criteria: LEAST RESTRAINT VIOLATION 
  • Olderado: 1GPX Olderado
Software Package:
Software NamePurpose
X-PLORphasing
X-PLORrefinement
X-PLORmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1999-01-27
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-11-29
    Type: Derived calculations, Other