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PDBsum entry 1xpw

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Structural genomics, unknown function PDB id
1xpw
Jmol
Contents
Protein chain
143 a.a. *
* Residue conservation analysis
PDB id:
1xpw
Name: Structural genomics, unknown function
Title: Solution nmr structure of human protein hspco34. Northeast structural genomics target hr1958
Structure: Loc51668 protein. Chain: a. Synonym: hspc034. Engineered: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Gene: pp25. Expressed in: escherichia coli. Expression_system_taxid: 562.
NMR struc: 20 models
Authors: T.A.Ramelot,R.Xiao,L.C.Ma,T.B.Acton,G.T.Montelione, M.A.Kennedy,Northeast Structural Genomics Consortium (Nesg)
Key ref:
T.A.Ramelot et al. (2009). Improving NMR protein structure quality by Rosetta refinement: a molecular replacement study. Proteins, 75, 147-167. PubMed id: 18816799 DOI: 10.1002/prot.22229
Date:
09-Oct-04     Release date:   09-Nov-04    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q9Y547  (HSB11_HUMAN) -  Intraflagellar transport protein 25 homolog
Seq:
Struc:
144 a.a.
143 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cell projection   5 terms 
  Biological process     left/right axis specification   10 terms 
  Biochemical function     metal ion binding     1 term  

 

 
DOI no: 10.1002/prot.22229 Proteins 75:147-167 (2009)
PubMed id: 18816799  
 
 
Improving NMR protein structure quality by Rosetta refinement: a molecular replacement study.
T.A.Ramelot, S.Raman, A.P.Kuzin, R.Xiao, L.C.Ma, T.B.Acton, J.F.Hunt, G.T.Montelione, D.Baker, M.A.Kennedy.
 
  ABSTRACT  
 
The structure of human protein HSPC034 has been determined by both solution nuclear magnetic resonance (NMR) spectroscopy and X-ray crystallography. Refinement of the NMR structure ensemble, using a Rosetta protocol in the absence of NMR restraints, resulted in significant improvements not only in structure quality, but also in molecular replacement (MR) performance with the raw X-ray diffraction data using MOLREP and Phaser. This method has recently been shown to be generally applicable with improved MR performance demonstrated for eight NMR structures refined using Rosetta (Qian et al., Nature 2007;450:259-264). Additionally, NMR structures of HSPC034 calculated by standard methods that include NMR restraints have improvements in the RMSD to the crystal structure and MR performance in the order DYANA, CYANA, XPLOR-NIH, and CNS with explicit water refinement (CNSw). Further Rosetta refinement of the CNSw structures, perhaps due to more thorough conformational sampling and/or a superior force field, was capable of finding alternative low energy protein conformations that were equally consistent with the NMR data according to the Recall, Precision, and F-measure (RPF) scores. On further examination, the additional MR-performance shortfall for NMR refined structures as compared with the X-ray structure were attributed, in part, to crystal-packing effects, real structural differences, and inferior hydrogen bonding in the NMR structures. A good correlation between a decrease in the number of buried unsatisfied hydrogen-bond donors and improved MR performance demonstrates the importance of hydrogen-bond terms in the force field for improving NMR structures. The superior hydrogen-bond network in Rosetta-refined structures demonstrates that correct identification of hydrogen bonds should be a critical goal of NMR structure refinement. Inclusion of nonbivalent hydrogen bonds identified from Rosetta structures as additional restraints in the structure calculation results in NMR structures with improved MR performance.
 
  Selected figure(s)  
 
Figure 1.
Figure 1. Structure of HSPC034. A: Secondary structure superimposed on sequence (adapted from PDBsum, http://www.ebi.ac.uk/thornton-srv/databases/pdbsum/). Residues that coordinate metal ions are marked with a blue dot. B: Ribbon representation of X-ray structure of HSPC034, residues 4-139. The Ca^+2 ion is shown in yellow and a Sm^+3 ion in green. C: Backbone atoms for 20 NMR structures optimally superimposed with respect the N, C , and C coordinates of the X-ray structure residues 6-138. NMR residues 2-141 are shown. D: NOE violations indicated on X-ray structure. Red violations are >2 Å, orange are 1-2 Å, and yellow are 0.5-1 Å. Violations are not show for residues 1-3 and 140-141. Figures (B-D) were generated using PyMOL (DeLano Scientific).
Figure 3.
Figure 3. Rosetta all atom energy versus backbone RMSD (residues 4-139) for NMR Rosetta refined structures (squares), and X-ray Rosetta refined structures with parallel (circles) and antiparallel (triangles) 1-strand structures.
 
  The above figures are reprinted by permission from John Wiley & Sons, Inc.: Proteins (2009, 75, 147-167) copyright 2009.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
22751672 T.C.Terwilliger, R.J.Read, P.D.Adams, A.T.Brunger, P.V.Afonine, R.W.Grosse-Kunstleve, and L.W.Hung (2012).
Improved crystallographic models through iterated local density-guided model deformation and reciprocal-space refinement.
  Acta Crystallogr D Biol Crystallogr, 68, 861-870.  
19921466 G.Kappé, W.C.Boelens, and W.W.de Jong (2010).
Why proteins without an alpha-crystallin domain should not be included in the human small heat shock protein family HSPB.
  Cell Stress Chaperones, 15, 457-461.  
20235548 K.W.Kaufmann, G.H.Lemmon, S.L.Deluca, J.H.Sheehan, and J.Meiler (2010).
Practically useful: what the Rosetta protein modeling suite can do for you.
  Biochemistry, 49, 2987-2998.  
20939100 S.Kalkhof, S.Haehn, M.Paulsson, N.Smyth, J.Meiler, and A.Sinz (2010).
Computational modeling of laminin N-terminal domains using sparse distance constraints from disulfide bonds and chemical cross-linking.
  Proteins, 78, 3409-3427.  
20000319 S.Raman, Y.J.Huang, B.Mao, P.Rossi, J.M.Aramini, G.Liu, G.T.Montelione, and D.Baker (2010).
Accurate automated protein NMR structure determination using unassigned NOESY data.
  J Am Chem Soc, 132, 202-207.  
19288278 G.T.Montelione, C.Arrowsmith, M.E.Girvin, M.A.Kennedy, J.L.Markley, R.Powers, J.H.Prestegard, and T.Szyperski (2009).
Unique opportunities for NMR methods in structural genomics.
  J Struct Funct Genomics, 10, 101-106.  
19805131 J.A.Vila, Y.A.Arnautova, O.A.Martin, and H.A.Scheraga (2009).
Quantum-mechanics-derived 13Calpha chemical shift server (CheShift) for protein structure validation.
  Proc Natl Acad Sci U S A, 106, 16972-16977.  
19382199 K.F.Lechtreck, S.Luro, J.Awata, and G.B.Witman (2009).
HA-tagging of putative flagellar proteins in Chlamydomonas reinhardtii identifies a novel protein of intraflagellar transport complex B.
  Cell Motil Cytoskeleton, 66, 469-482.  
19422060 M.Schneider, X.Fu, and A.E.Keating (2009).
X-ray vs. NMR structures as templates for computational protein design.
  Proteins, 77, 97.  
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.