2GVA

REFINED SOLUTION STRUCTURE OF THE TYR 41--> HIS MUTANT OF THE M13 GENE V PROTEIN. A COMPARISON WITH THE CRYSTAL STRUCTURE


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Submitted: 30 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Refined solution structure of the Tyr41-->His mutant of the M13 gene V protein. A comparison with the crystal structure.

Prompers, J.J.Folmer, R.H.Nilges, M.Folkers, P.J.Konings, R.N.Hilbers, C.W.

(1995) Eur J Biochem 232: 506-514

  • Primary Citation of Related Structures:  
    2GVA, 2GVB

  • PubMed Abstract: 

    The three-dimensional solution structure of mutant Tyr41-->His of the single-stranded DNA binding protein encoded by gene V of the filamentous bacteriophage M13 has been refined in two stages. The first stage involved the collection of additional NOE-based distance constraints, which were then used in eight cycles of back-calculations and structure calculations. The structures of the gene V protein dimers were calculated using simulated annealing, employing restrained molecular dynamics with a geometric force field. In the second stage of the refinement procedure, solvent was explicitly included during the dynamic calculations. A total of 30 structures was calculated for the protein, representing its solution structure in water. The first calculation step significantly improved the convergence of the structures, whereas the subsequent simulations in water made the structures physically more realistic. This is, for instance, illustrated by the number of hydrogen bonds formed in the molecule, which increased considerably upon going to aqueous solution. It is shown that the solution structure of the mutant gene V protein is nearly identical to the crystal structure of the wild-type molecule, except for the DNA-binding loop (residues 16-28). This antiparallel beta-hairpin is twisted and partially folded back towards the core of the protein in the NMR structure, whereas it is more extended and points away from the rest of the molecule in the X-ray structure. Unrestrained molecular dynamics calculations suggest that this latter conformation is energetically unstable in solution.


  • Organizational Affiliation

    Nijmegen Son Research Center, University of Nijmegen, The Netherlands.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
GENE V PROTEIN
A, B
87Inovirus M13Mutation(s): 0 
UniProt
Find proteins for P69544 (Enterobacteria phage M13)
Explore P69544 
Go to UniProtKB:  P69544
Entity Groups  
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UniProt GroupP69544
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Submitted: 30 

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1995-10-15
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2022-03-09
    Changes: Database references, Derived calculations, Other
  • Version 1.4: 2024-05-29
    Changes: Data collection