Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Submitted: 40 

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history


Solution-state structure by NMR of zinc-substituted rubredoxin from the marine hyperthermophilic archaebacterium Pyrococcus furiosus.

Blake, P.R.Park, J.B.Zhou, Z.H.Hare, D.R.Adams, M.W.Summers, M.F.

(1992) Protein Sci. 1: 1508-1521

  • DOI: 10.1002/pro.5560011112

  • PubMed Abstract: 
  • The three-dimensional solution-state structure is reported for the zinc-substituted form of rubredoxin (Rd) from the marine hyperthermophilic archaebacterium Pyrococcus furiosus, an organism that grows optimally at 100 degrees C. Structures were gene ...

    The three-dimensional solution-state structure is reported for the zinc-substituted form of rubredoxin (Rd) from the marine hyperthermophilic archaebacterium Pyrococcus furiosus, an organism that grows optimally at 100 degrees C. Structures were generated with DSPACE by a hybrid distance geometry (DG)-based simulated annealing (SA) approach that employed 403 nuclear Overhauser effect (NOE)-derived interproton distance restraints, including 67 interresidue, 124 sequential (i-j = 1), 75 medium-range (i-j = 2-5), and 137 long-range (i-j > 5) restraints. All lower interproton distance bounds were set at the sum of the van Der Waals radii (1.8 A), and upper bounds of 2.7 A, 3.3 A, and 5.0 A were employed to represent qualitatively observed strong, medium, and weak NOE cross peak intensities, respectively. Twenty-three backbone-backbone, six backbone-sulfur (Cys), two backbone-side chain, and two side chain-side chain hydrogen bond restraints were include for structure refinement, yielding a total of 436 nonbonded restraints, which averages to > 16 restraints per residue. A total of 10 structures generated from random atom positions and 30 structures generated by molecular replacement using the backbone coordinates of Clostridium pasteurianum Rd converged to a common conformation, with the average penalty (= sum of the square of the distance bounds violations; +/- standard deviation) of 0.024 +/- 0.003 A2 and a maximum total penalty of 0.035 A2. Superposition of the backbone atoms (C, C alpha, N) of residues A1-L51 for all 40 structures afforded an average pairwise root mean square (rms) deviation value (+/- SD) of 0.42 +/- 0.07 A. Superposition of all heavy atoms for residues A1-L51, including those of structurally undefined external side chains, afforded an average pairwise rms deviation of 0.72 +/- 0.08 A. Qualitative comparison of back-calculated and experimental two-dimensional NOESY spectra indicate that the DG/SA structures are consistent with the experimental spectra. The global folding of P. furiosus Zn(Rd) is remarkably similar to the folding observed by X-ray crystallography for native Rd from the mesophilic organism C. pasteurianum, with the average rms deviation value for backbone atoms of residues A1-L51 of P. furiosus Zn(Rd) superposed with respect to residues K2-V52 of C. pasteurianum Rd of 0.77 +/- 0.06 A. The conformations of aromatic residues that compose the hydrophobic cores of the two proteins are also similar. However, P. furiosus Rd contains several unique structural elements, including at least four additional hydrogen bonds and three potential electrostatic interactions.(ABSTRACT TRUNCATED AT 400 WORDS)

    Related Citations: 
    • Determinants of Protein Hyperthermostability: Purification and Amino Acid Sequence of Rubredoxin from the Hyperthermophilic Archaebacterium Pyrococcus Furiosus and Secondary Structure of the Zinc Adduct by NMR
      Blake, P.R.,Park, J.-B.,Bryant, F.O.,Aono, S.,Magnuson, J.K.,Eccleston, E.,Howard, J.B.,Summers, M.F.,Adams, M.W.W.
      (1991) Biochemistry 30: 10885
    • Quantitative Measurement of Small Through-Hydrogen-Bond and 'Through-Space' 1H-113Cd and 1H-199Hg J Couplings in Metal-Substituted Rubredoxin from Pyrococcus Furiosus
      Blake, P.R.,Lee, B.,Summers, M.F.,Adams, M.W.,Park, J.B.,Zhou, Z.H.,Bax, A.
      (1992) J.Biomol.NMR 2: 527
    • Comparison of the X-Ray Structure of Native Rubredoxin from Pyrococcus Furiosus with the NMR Structure of the Zinc-Substituted Protein
      Blake, P.R.,Day, M.W.,Hsu, B.T.,Joshua-Tor, L.,Park, J.-B.,Hare, D.R.,Adams, M.W.W.,Rees, D.C.,Summers, M.F.
      (1992) Protein Sci. 1: 1522
    • Novel Observation of Nh...S(Cys) Hydrogen-Bond-Mediated Scalar Coupling in 113Cd-Substituted Rubredoxin from Pyrococcus Furiosus
      Blake, P.R.,Park, J.B.,Adams, M.W.W.,Summers, M.F.
      (1992) J.Am.Chem.Soc. 114: 4931

    Organizational Affiliation

    Department of Chemistry and Biochemistry, University of Maryland Baltimore County 21228.


Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
53Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)Mutation(s): 0 
Gene Names: rub
Find proteins for P24297 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1))
Go to UniProtKB:  P24297
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
Query on ZN

Download SDF File 
Download CCD File 
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Submitted: 40 
  • Olderado: 1ZRP Olderado

Structure Validation

View Full Validation Report or Ramachandran Plots

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1993-10-31
    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