1TVG

X-ray structure of human PP25 gene product, HSPC034. Northeast Structural Genomics Target HR1958.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.215 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Improving NMR protein structure quality by Rosetta refinement: a molecular replacement study.

Ramelot, T.A.Raman, S.Kuzin, A.P.Xiao, R.Ma, L.C.Acton, T.B.Hunt, J.F.Montelione, G.T.Baker, D.Kennedy, M.A.

(2009) Proteins 75: 147-167

  • DOI: 10.1002/prot.22229
  • Primary Citation of Related Structures:  

  • PubMed 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, ...

    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.


    Organizational Affiliation

    Department of Chemistry and Biochemistry and Northeast Structural Genomics Consortium, Miami University, Oxford, Ohio 45056, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
LOC51668 protein
A
153Homo sapiensMutation(s): 0 
Gene Names: HSPB11 (C1orf41, IFT25)
Find proteins for Q9Y547 (Homo sapiens)
Go to Gene View: HSPB11
Go to UniProtKB:  Q9Y547
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SM
Query on SM

Download SDF File 
Download CCD File 
A
SAMARIUM (III) ION
Sm
DOSGOCSVHPUUIA-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download SDF File 
Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.215 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 70.974α = 90.00
b = 41.617β = 102.19
c = 46.779γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
SOLVEphasing
CNSrefinement
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-11-09
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance