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PDBsum entry 1a2p
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* Residue conservation analysis
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DOI no:
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Acta Crystallogr D Biol Crystallogr
55:386-398
(1999)
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PubMed id:
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Refinement and structural analysis of barnase at 1.5 A resolution.
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C.Martin,
V.Richard,
M.Salem,
R.Hartley,
Y.Mauguen.
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ABSTRACT
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The structure of Bacillus amyloliquefaciens ribonuclease (barnase), an
extracellular 110-residue enzyme initially solved at 2.0 A resolution, has been
refined at 1.5 A using synchrotron radiation and an imaging-plate scanner.
Refinement with anisotropic atomic displacement parameters resulted in increased
accuracy of the structure. The final model has a crystallographic R factor of
11.5% and an Rfree of 17.4%. The three independent molecules in the asymmetric
unit, referred to as A, B and C, allowed detailed analysis of this final model
and meaningful comparison with structures of barnase complexed either with
nucleotide inhibitors or with its natural intracellular inhibitor, barstar. The
analysis of the overall solvent structure revealed a similar number of water
molecules associated with each barnase molecule; among these were 16 equivalent
buried solvent molecules, the locations of which are discussed in detail and
classified on the basis of their structural role. The importance of the water
molecules' contribution to the barnase-barstar interaction is also highlighted.
The high accuracy of the present analysis revealed the presence of a Zn2+ ion
mediating the contacts between pairs of symmetry-related A, B or C molecules;
such an ion had previously only been identified for pairs of C molecules.
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Selected figure(s)
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Figure 5.
Figure 5 Ser38A with two alternative conformations in (3F[o] -
2F[c],  c)
electron-density map contoured at 0.05 e Å^-3 (1  ).
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Figure 10.
Figure 10 Stereoview of buried water molecules located in the
catalytic site as seen in a (F[o] - F[c]) map, contoured at 2
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with waters omitted from the structure-factor calculation.
Dashed lines show hydrogen bonds.
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The above figures are
reprinted
by permission from the IUCr:
Acta Crystallogr D Biol Crystallogr
(1999,
55,
386-398)
copyright 1999.
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Figures were
selected
by an automated process.
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Literature references that cite this PDB file's key reference
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Google scholar
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PubMed id
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Reference
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S.Wells,
S.Menor,
B.Hespenheide,
and
M.F.Thorpe
(2005).
Constrained geometric simulation of diffusive motion in proteins.
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Phys Biol,
2,
S127-S136.
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J.Giraldo,
L.De Maria,
and
S.J.Wodak
(2004).
Shift in nucleotide conformational equilibrium contributes to increased rate of catalysis of GpAp versus GpA in barnase.
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Proteins,
56,
261-276.
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R.E.Georgescu,
E.G.Alexov,
and
M.R.Gunner
(2002).
Combining conformational flexibility and continuum electrostatics for calculating pK(a)s in proteins.
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Biophys J,
83,
1731-1748.
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S.B.Nolde,
A.S.Arseniev,
V.Y.Orekhov,
and
M.Billeter
(2002).
Essential domain motions in barnase revealed by MD simulations.
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Proteins,
46,
250-258.
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L.P.Lee,
and
B.Tidor
(2001).
Optimization of binding electrostatics: charge complementarity in the barnase-barstar protein complex.
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Protein Sci,
10,
362-377.
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The most recent references are shown first.
Citation data come partly from CiteXplore and partly
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