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PDBsum entry 1lzt
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Hydrolase(o-glycosyl)
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PDB id
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1lzt
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Contents |
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* Residue conservation analysis
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Enzyme class:
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E.C.3.2.1.17
- lysozyme.
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Reaction:
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Hydrolysis of the 1,4-beta-linkages between N-acetyl-D-glucosamine and N-acetylmuramic acid in peptidoglycan heteropolymers of the prokaryotes cell walls.
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Acta Crystallogr B
46:54-62
(1990)
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PubMed id:
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Refinement of triclinic lysozyme: I. Fourier and least-squares methods.
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J.M.Hodsdon,
G.M.Brown,
L.C.Sieker,
L.H.Jensen.
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ABSTRACT
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X-ray diffraction data to 1.5 A resolution have been collected for triclinic
crystals of hen egg white lysozyme. The triclinic model was derived from the
tetragonal one by the rotation function and refined initially by Fo-Fc and
differential difference syntheses against 2 A resolution data. Refinement was
continued by differential difference cycles against the 1.5 A data until R was
reduced to 0.220. Although the initial refinement was rapid, it was subsequently
a matter of attrition, leading to a complete recheck of the data and the
discovery of systematic error which affected primarily the high-resolution data.
Refinement was continued against the corrected 2 A data by block-diagonal least
squares. After five cycles the refinement was terminated at R = 0.254 because of
the imminent availability of a preferred refinement program. Problems with the
protein model, the solvent, and the interaction of the scale and thermal
parameters are discussed. The experiences gained in this study are summarized.
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Literature references that cite this PDB file's key reference
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PubMed id
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Reference
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L.Ito,
K.Shiraki,
T.Matsuura,
M.Okumura,
K.Hasegawa,
S.Baba,
H.Yamaguchi,
and
T.Kumasaka
(2011).
High-resolution X-ray analysis reveals binding of arginine to aromatic residues of lysozyme surface: implication of suppression of protein aggregation by arginine.
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Protein Eng Des Sel,
24,
269-274.
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PDB codes:
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J.de Ruyck,
Y.Oudjama,
and
J.Wouters
(2008).
Monoclinic form of isopentenyl diphosphate isomerase: a case of polymorphism in biomolecular crystals.
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Acta Crystallogr Sect F Struct Biol Cryst Commun,
64,
239-242.
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PDB codes:
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A.Bottoni,
G.P.Miscione,
and
M.De Vivo
(2005).
A theoretical DFT investigation of the lysozyme mechanism: computational evidence for a covalent intermediate pathway.
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Proteins,
59,
118-130.
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A.M.Deacon,
C.M.Weeks,
R.Miller,
and
S.E.Ealick
(1998).
The Shake-and-Bake structure determination of triclinic lysozyme.
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Proc Natl Acad Sci U S A,
95,
9284-9289.
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G.Otting,
E.Liepinsh,
B.Halle,
and
U.Frey
(1997).
NMR identification of hydrophobic cavities with low water occupancies in protein structures using small gas molecules.
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Nat Struct Biol,
4,
396-404.
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T.J.You,
and
D.Bashford
(1995).
Conformation and hydrogen ion titration of proteins: a continuum electrostatic model with conformational flexibility.
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Biophys J,
69,
1721-1733.
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C.P.Hill,
N.L.Johnston,
and
R.E.Cohen
(1993).
Crystal structure of a ubiquitin-dependent degradation substrate: a three-disulfide form of lysozyme.
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Proc Natl Acad Sci U S A,
90,
4136-4140.
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PDB code:
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The most recent references are shown first.
Citation data come partly from CiteXplore and partly
from an automated harvesting procedure. Note that this is likely to be
only a partial list as not all journals are covered by
either method. However, we are continually building up the citation data
so more and more references will be included with time.
Where a reference describes a PDB structure, the PDB
codes are
shown on the right.
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Links
