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PDBsum entry 2vb1
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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
63:1254-1268
(2007)
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PubMed id:
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Triclinic lysozyme at 0.65 A resolution.
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J.Wang,
M.Dauter,
R.Alkire,
A.Joachimiak,
Z.Dauter.
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ABSTRACT
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The crystal structure of triclinic hen egg-white lysozyme (HEWL) has been
refined against diffraction data extending to 0.65 A resolution measured at 100
K using synchrotron radiation. Refinement with anisotropic displacement
parameters and with the removal of stereochemical restraints for the well
ordered parts of the structure converged with a conventional R factor of 8.39%
and an R(free) of 9.52%. The use of full-matrix refinement provided an estimate
of the variances in the derived parameters. In addition to the 129-residue
protein, a total of 170 water molecules, nine nitrate ions, one acetate ion and
three ethylene glycol molecules were located in the electron-density map. Eight
sections of the main chain and many side chains were modeled with alternate
conformations. The occupancies of the water sites were refined and this step is
meaningful when assessed by use of the free R factor. A detailed description and
comparison of the structure are made with reference to the previously reported
triclinic HEWL structures refined at 0.925 A (at the low temperature of 120 K)
and at 0.95 A resolution (at room temperature).
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Selected figure(s)
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Figure 5.
Figure 5 (a) Distribution of the N-C^  -C
angles for the current model and (b) for 3lzt . (c) Modeling the
peptide flip around Asn103 in 3lzt and (d) in the current model.
Blue and red colours in (a) correspond to residues in single and
double conformations, respectively.
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Figure 9.
Figure 9 Distributions of peptide-bond lengths for well ordered
parts of the model. Red columns represent restrained refinement
and green columns unrestrained refinement.
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The above figures are
reprinted
by permission from the IUCr:
Acta Crystallogr D Biol Crystallogr
(2007,
63,
1254-1268)
copyright 2007.
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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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A.Higashiura,
T.Kurakane,
M.Matsuda,
M.Suzuki,
K.Inaka,
M.Sato,
T.Kobayashi,
T.Tanaka,
H.Tanaka,
K.Fujiwara,
and
A.Nakagawa
(2010).
High-resolution X-ray crystal structure of bovine H-protein at 0.88 A resolution.
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Acta Crystallogr D Biol Crystallogr,
66,
698-708.
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PDB code:
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B.Reiz,
and
L.Li
(2010).
Microwave-assisted acid and base hydrolysis of intact proteins containing disulfide bonds for protein sequence analysis by mass spectrometry.
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J Am Soc Mass Spectrom,
21,
1596-1605.
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C.A.Velikovsky,
L.Deng,
S.Tasumi,
L.M.Iyer,
M.C.Kerzic,
L.Aravind,
Z.Pancer,
and
R.A.Mariuzza
(2009).
Structure of a lamprey variable lymphocyte receptor in complex with a protein antigen.
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Nat Struct Mol Biol,
16,
725-730.
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PDB codes:
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W.Bialek,
S.Krzywda,
M.Jaskolski,
and
A.Szczepaniak
(2009).
Atomic-resolution structure of reduced cyanobacterial cytochrome c6 with an unusual sequence insertion.
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FEBS J,
276,
4426-4436.
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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
