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PDBsum entry 2gvb
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DNA-binding (viral)
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PDB id
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2gvb
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Contents |
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* Residue conservation analysis
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References listed in PDB file
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Key reference
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Title
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Refined solution structure of the tyr41--≫his mutant of the m13 gene V protein. A comparison with the crystal structure.
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Authors
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J.J.Prompers,
R.H.Folmer,
M.Nilges,
P.J.Folkers,
R.N.Konings,
C.W.Hilbers.
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Ref.
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Eur J Biochem, 1995,
232,
506-514.
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PubMed id
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Abstract
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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.
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Secondary reference #1
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Title
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The solution structure of the tyr41--≫his mutant of the single-Stranded DNA binding protein encoded by gene V of the filamentous bacteriophage m13.
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Authors
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P.J.Folkers,
M.Nilges,
R.H.Folmer,
R.N.Konings,
C.W.Hilbers.
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Ref.
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J Mol Biol, 1994,
236,
229-246.
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PubMed id
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Secondary reference #2
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Title
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Exploring the DNA binding domain of gene V protein encoded by bacteriophage m13 with the aid of spin-Labeled oligonucleotides in combination with 1h-Nmr.
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Authors
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P.J.Folkers,
J.P.Van duynhoven,
H.T.Van lieshout,
B.J.Harmsen,
J.H.Van boom,
G.I.Tesser,
R.N.Konings,
C.W.Hilbers.
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Ref.
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Biochemistry, 1993,
32,
9407-9416.
[DOI no: ]
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PubMed id
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Secondary reference #3
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Title
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Sequence-Specific 1h-Nmr assignment and secondary structure of the tyr41----His mutant of the single-Stranded DNA binding protein, Gene V protein, Encoded by the filamentous bacteriophage m13.
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Authors
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P.J.Folkers,
J.P.Van duynhoven,
A.J.Jonker,
B.J.Harmsen,
R.N.Konings,
C.W.Hilbers.
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Ref.
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Eur J Biochem, 1991,
202,
349-360.
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PubMed id
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Secondary reference #4
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Title
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Characterization of wild-Type and mutant m13 gene V proteins by means of 1h-Nmr.
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Authors
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P.J.Folkers,
A.P.Stassen,
J.P.Van duynhoven,
B.J.Harmsen,
R.N.Konings,
C.W.Hilbers.
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Ref.
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Eur J Biochem, 1991,
200,
139-148.
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PubMed id
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