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PDBsum entry 1jsf
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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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Proteins
30:232-243
(1998)
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PubMed id:
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Full-matrix least-squares refinement of lysozymes and analysis of anisotropic thermal motion.
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K.Harata,
Y.Abe,
M.Muraki.
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ABSTRACT
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Crystal structures of turkey egg lysozyme (TEL) and human lysozyme (HL) were
refined by full-matrix least-squares method using anisotropic temperature
factors. The refinement converged at the conventional R-values of 0.104 (TEL)
and 0.115 (HL) for reflections with Fo > 0 to the resolution of 1.12 A and
1.15 A, respectively. The estimated r.m.s. coordinate errors for protein atoms
were 0.031 A (TEL) and 0.034 A (HL). The introduction of anisotropic temperature
factors markedly reduced the R-value but did not significantly affect the main
chain coordinates. The degree of anisotropy of atomic thermal motion has strong
positive correlation with the square of distance from the molecular centroid.
The ratio of the radial component of thermal ellipsoid to the r.m.s. magnitude
of three principal components has negative correlation with the distance from
the molecular centroid, suggesting the domination of libration rather than
breathing motion. The TLS model was applied to elucidate the characteristics of
the rigid-body motion. The TLS tensors were determined by the least-squares fit
to observed temperature factors. The profile of the magnitude of reproduced
temperature factors by the TLS method well fitted to that of observed B(eqv).
However, considerable disagreement was observed in the shape and orientation of
thermal ellipsoid for atoms with large temperature factors, indicating the large
contribution of local motion. The upper estimate of the external motion, 67%
(TEL) and 61% (HL) of B(eqv), was deduced from the plot of the magnitude of TLS
tensors determined for main chain atoms which were grouped into shells according
to the distance from the center of libration. In the external motion, the
translational portion is predominant and the contribution of libration and screw
motion is relatively small. The internal motion, estimated by subtracting the
upper estimate of the external motion from the observed temperature factor, is
very similar between TEL and HL in spite of the difference in 54 of 130 amino
acid residues and in crystal packing, being suggested to reflect the intrinsic
internal motion of chicken-type lysozymes.
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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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J.A.Doebbler,
and
R.B.Von Dreele
(2009).
Application of molecular replacement to protein powder data from image plates.
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Acta Crystallogr D Biol Crystallogr,
65,
348-355.
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J.Hakanpää,
M.Linder,
A.Popov,
A.Schmidt,
and
J.Rouvinen
(2006).
Hydrophobin HFBII in detail: ultrahigh-resolution structure at 0.75 A.
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Acta Crystallogr D Biol Crystallogr,
62,
356-367.
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PDB code:
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D.Vitkup,
D.Ringe,
M.Karplus,
and
G.A.Petsko
(2002).
Why protein R-factors are so large: a self-consistent analysis.
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Proteins,
46,
345-354.
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K.Harata,
and
R.Kanai
(2002).
Crystallographic dissection of the thermal motion of protein-sugar complex.
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Proteins,
48,
53-62.
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PDB code:
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M.S.Yousef,
F.Fabiola,
J.L.Gattis,
T.Somasundaram,
and
M.S.Chapman
(2002).
Refinement of the arginine kinase transition-state analogue complex at 1.2 A resolution: mechanistic insights.
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Acta Crystallogr D Biol Crystallogr,
58,
2009-2017.
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PDB code:
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M.D.Winn,
M.N.Isupov,
and
G.N.Murshudov
(2001).
Use of TLS parameters to model anisotropic displacements in macromolecular refinement.
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Acta Crystallogr D Biol Crystallogr,
57,
122-133.
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U.Das,
S.Chen,
M.Fuxreiter,
A.A.Vaguine,
J.Richelle,
H.M.Berman,
and
S.J.Wodak
(2001).
Checking nucleic acid crystal structures.
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Acta Crystallogr D Biol Crystallogr,
57,
813-828.
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M.Arai,
P.Hamel,
E.Kanaya,
K.Inaka,
K.Miki,
M.Kikuchi,
and
K.Kuwajima
(2000).
Effect of an alternative disulfide bond on the structure, stability, and folding of human lysozyme.
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Biochemistry,
39,
3472-3479.
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Y.Nishimiya,
K.Tsumoto,
M.Shiroishi,
K.Yutani,
and
I.Kumagai
(2000).
Thermodynamic consequences of grafting enhanced affinity toward the mutated antigen onto an antibody. The case of anti-lysozyme antibody, HyHEL-10.
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J Biol Chem,
275,
12813-12820.
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E.A.Merritt
(1999).
Expanding the model: anisotropic displacement parameters in protein structure refinement.
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Acta Crystallogr D Biol Crystallogr,
55,
1109-1117.
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O.Carugo,
and
P.Argos
(1999).
Reliability of atomic displacement parameters in protein crystal structures.
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Acta Crystallogr D Biol Crystallogr,
55,
473-478.
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T.Sandalova,
G.Schneider,
H.Käck,
and
Y.Lindqvist
(1999).
Structure of dethiobiotin synthetase at 0.97 A resolution.
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Acta Crystallogr D Biol Crystallogr,
55,
610-624.
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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
code is
shown on the right.
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Links
