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PDBsum entry 5jtw
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Immune system
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PDB id
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5jtw
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Contents |
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651 a.a.
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632 a.a.
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281 a.a.
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References listed in PDB file
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Key reference
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Title
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Re-Evaluation of low-Resolution crystal structures via interactive molecular-Dynamics flexible fitting (imdff): a case study in complement c4.
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Authors
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T.I.Croll,
G.R.Andersen.
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Ref.
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Acta Crystallogr D Struct Biol, 2016,
72,
1006-1016.
[DOI no: ]
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PubMed id
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Abstract
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While the rapid proliferation of high-resolution structures in the Protein Data
Bank provides a rich set of templates for starting models, it remains the case
that a great many structures both past and present are built at least in part by
hand-threading through low-resolution and/or weak electron density. With current
model-building tools this task can be challenging, and the de facto standard for
acceptable error rates (in the form of atomic clashes and unfavourable backbone
and side-chain conformations) in structures based on data with dmax not
exceeding 3.5 Å reflects this. When combined with other factors such as model
bias, these residual errors can conspire to make more serious errors in the
protein fold difficult or impossible to detect. The three recently published
3.6-4.2 Å resolution structures of complement C4 (PDB entries 4fxg, 4fxk and
4xam) rank in the top quartile of structures of comparable resolution both in
terms of Rfree and MolProbity score, yet, as shown here, contain register errors
in six β-strands. By applying a molecular-dynamics force field that explicitly
models interatomic forces and hence excludes most physically impossible
conformations, the recently developed interactive molecular-dynamics flexible
fitting (iMDFF) approach significantly reduces the complexity of the
conformational space to be searched during manual rebuilding. This substantially
improves the rate of detection and correction of register errors, and allows
user-guided model building in maps with a resolution lower than 3.5 Å to
converge to solutions with a stereochemical quality comparable to atomic
resolution structures. Here, iMDFF has been used to individually correct and
re-refine these three structures to MolProbity scores of <1.7, and strategies
for working with such challenging data sets are suggested. Notably, the improved
model allowed the resolution for complement C4b to be extended from 4.2 to
3.5 Å as demonstrated by paired refinement.
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Secondary reference #1
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Title
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Structural basis for the function of complement component c4 within the classical and lectin pathways of complement.
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Authors
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S.Mortensen,
R.T.Kidmose,
S.V.Petersen,
..Szilágyi,
Z.Prohászka,
G.R.Andersen.
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Ref.
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J Immunol, 2015,
194,
5488-5496.
[DOI no: ]
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PubMed id
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