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PDBsum entry 1lsb
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Hydrolase(o-glycosyl)
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PDB id
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1lsb
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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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DOI no:
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Acta Crystallogr D Biol Crystallogr
51:98
(1995)
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PubMed id:
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The influence of temperature on lysozyme crystals. Structure and dynamics of protein and water.
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I.V.Kurinov,
R.W.Harrison.
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ABSTRACT
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Lysozyme structures at six different temperatures in the range 95-295 K have
been determined using X-ray crystallography at a resolution of 1.7 A. The
crystals at lower temperatures had a 7.4% decrease in the unit-cell volume. The
volume change was discontinuous with the volume being near 238 000 A(3) from 295
to 250 K and about 220 200 A(3) below 180 K. The thermal expansion of the
protein has been analyzed and shows anisotropy, which is correlated with local
atomic packing and secondary-structure elements. The lysozyme structure at low
temperature is nearly the same as that at high temperature, with only small
relative translations and rotations of structure elements including a
hinge-bending rearrangement of two domains. Because of a considerable increase
of lattice disorder at low temperature dynamical analysis of internal motion is
difficult. The analysis of structural and dynamical properties of well ordered
protein-bound water has been carried out.
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Selected figure(s)
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Figure 6.
Fig. 6. Average thermal expansion coefficient of protein, tr(T~, T2)
x 10 -4 K-~, as a function of residue number.
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Figure 7.
Fig. 7. Temperature dependence of calculated accessible surface
area (/k 2) of lysozyme, using a 1.6 A radius probe.
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The above figures are
reprinted
by permission from the IUCr:
Acta Crystallogr D Biol Crystallogr
(1995,
51,
98-0)
copyright 1995.
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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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PubMed id
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Reference
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C.Rajendran,
F.S.Dworkowski,
M.Wang,
and
C.Schulze-Briese
(2011).
Radiation damage in room-temperature data acquisition with the PILATUS 6M pixel detector.
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J Synchrotron Radiat,
18,
318-328.
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G.Bujacz,
B.Wrzesniewska,
and
A.Bujacz
(2010).
Cryoprotection properties of salts of organic acids: a case study for a tetragonal crystal of HEW lysozyme.
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Acta Crystallogr D Biol Crystallogr,
66,
789-796.
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M.Weik,
and
J.P.Colletier
(2010).
Temperature-dependent macromolecular X-ray crystallography.
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Acta Crystallogr D Biol Crystallogr,
66,
437-446.
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B.R.Donald,
and
J.Martin
(2009).
Automated NMR Assignment and Protein Structure Determination using Sparse Dipolar Coupling Constraints.
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Prog Nucl Magn Reson Spectrosc,
55,
101-127.
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K.Hinsen
(2008).
Structural flexibility in proteins: impact of the crystal environment.
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Bioinformatics,
24,
521-528.
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X.Chen,
I.Weber,
and
R.W.Harrison
(2008).
Hydration water and bulk water in proteins have distinct properties in radial distributions calculated from 105 atomic resolution crystal structures.
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J Phys Chem B,
112,
12073-12080.
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B.Halle
(2004).
Biomolecular cryocrystallography: structural changes during flash-cooling.
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Proc Natl Acad Sci U S A,
101,
4793-4798.
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C.J.Langmead,
A.Yan,
R.Lilien,
L.Wang,
and
B.R.Donald
(2004).
A polynomial-time nuclear vector replacement algorithm for automated NMR resonance assignments.
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J Comput Biol,
11,
277-298.
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V.A.Higman,
J.Boyd,
L.J.Smith,
and
C.Redfield
(2004).
Asparagine and glutamine side-chain conformation in solution and crystal: a comparison for hen egg-white lysozyme using residual dipolar couplings.
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J Biomol NMR,
30,
327-346.
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H.Urabe,
Y.Sugawara,
M.Ataka,
and
A.Rupprecht
(1998).
Low-frequency Raman spectra of lysozyme crystals and oriented DNA films: dynamics of crystal water.
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Biophys J,
74,
1533-1540.
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S.D.Rader,
and
D.A.Agard
(1997).
Conformational substates in enzyme mechanism: the 120 K structure of alpha-lytic protease at 1.5 A resolution.
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Protein Sci,
6,
1375-1386.
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PDB codes:
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D.R.Davies,
and
G.H.Cohen
(1996).
Interactions of protein antigens with antibodies.
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Proc Natl Acad Sci U S A,
93,
7.
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S.Chacko,
E.W.Silverton,
S.J.Smith-Gill,
D.R.Davies,
K.A.Shick,
K.A.Xavier,
R.C.Willson,
P.D.Jeffrey,
C.Y.Chang,
L.C.Sieker,
and
S.Sheriff
(1996).
Refined structures of bobwhite quail lysozyme uncomplexed and complexed with the HyHEL-5 Fab fragment.
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Proteins,
26,
55-65.
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PDB codes:
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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
