1YGW

NMR STRUCTURE OF RIBONUCLEASE T1, 34 STRUCTURES


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 50 
  • Conformers Submitted: 34 
  • Selection Criteria: SEE JRNL REFERENCE 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Limits of NMR structure determination using variable target function calculations: ribonuclease T1, a case study.

Pfeiffer, S.Karimi-Nejad, Y.Ruterjans, H.

(1997) J.Mol.Biol. 266: 400-423

  • DOI: 10.1006/jmbi.1996.0784

  • PubMed Abstract: 
  • Limits of NMR structure determination using multidimensional NMR spectroscopy, variable target function calculations and relaxation matrix analysis were explored using the model protein ribonuclease T1 (RNase T1). The enzyme consists of 104 amino aci ...

    Limits of NMR structure determination using multidimensional NMR spectroscopy, variable target function calculations and relaxation matrix analysis were explored using the model protein ribonuclease T1 (RNase T1). The enzyme consists of 104 amino acid residues and has a molecular mass of approximately 11 kDa. Primary experimental data comprise 1856 assigned NOE intensities, 493 3J coupling constants and 62 values of amid proton exchange rates. From these data, 2580 distance bounds, 168 allowed ranges for torsional angles and stereospecific assignments for 75% of beta-methylene protons as well as for 80% of diastereotopic methyl groups were derived. Whenever possible, the distance restraints were refined in a relaxation matrix analysis including amid proton exchange data for improvement of lower distance limits. Description of side-chain conformations were based on various models of motional averaging of 3J coupling constants. The final structure ensemble was selected from the starting ensemble comparing the global precision of structures with order parameters derived from 15N relaxation time measurements. Significant differences between the structure of RNase T1 in solution and in the crystal became apparent from a comparison of the two highly resolved structures.


    Related Citations: 
    • Conformation of Valine Side Chains in Ribonuclease T1 Determined by NMR Studies of Homonuclear and Heteronuclear 3J Coupling Constants
      Karimi-Nejad, Y.,Schmidt, J.M.,Ruterjans, H.,Schwalbe, H.,Griesinger, C.
      (1994) Biochemistry 33: 5481
    • Complete 1H, 15N and 13C Resonance Assignment of Ribonuclease T1: Secondary Structure and Backbone Dynamics as Derived from the Chemical Shifts
      Pfeiffer, S.,Engelke, J.,Ruterjans, H.
      (1996) Q.Magn.Reson.Biol.Med. 3: 69


    Organizational Affiliation

    Institut für Biophysikalische Chemie, Johann Wolfgang Goethe-Universität, Biozentrum, Frankfurt, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
RIBONUCLEASE T1
A
104Aspergillus oryzae (strain ATCC 42149 / RIB 40)Mutation(s): 0 
Gene Names: rntA
EC: 3.1.27.3
Find proteins for P00651 (Aspergillus oryzae (strain ATCC 42149 / RIB 40))
Go to UniProtKB:  P00651
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 50 
  • Conformers Submitted: 34 
  • Selection Criteria: SEE JRNL REFERENCE 
  • Olderado: 1YGW Olderado

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1997-10-08
    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