4XOF

Observing the overall rocking motion of a protein in a crystal - Orthorhombic Ubiquitin crystals without Zinc.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.15 Å
  • R-Value Free: 0.171 
  • R-Value Work: 0.137 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Observing the overall rocking motion of a protein in a crystal.

Ma, P.Xue, Y.Coquelle, N.Haller, J.D.Yuwen, T.Ayala, I.Mikhailovskii, O.Willbold, D.Colletier, J.P.Skrynnikov, N.R.Schanda, P.

(2015) Nat Commun 6: 8361-8361

  • DOI: 10.1038/ncomms9361
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The large majority of three-dimensional structures of biological macromolecules have been determined by X-ray diffraction of crystalline samples. High-resolution structure determination crucially depends on the homogeneity of the protein crystal. Ove ...

    The large majority of three-dimensional structures of biological macromolecules have been determined by X-ray diffraction of crystalline samples. High-resolution structure determination crucially depends on the homogeneity of the protein crystal. Overall 'rocking' motion of molecules in the crystal is expected to influence diffraction quality, and such motion may therefore affect the process of solving crystal structures. Yet, so far overall molecular motion has not directly been observed in protein crystals, and the timescale of such dynamics remains unclear. Here we use solid-state NMR, X-ray diffraction methods and μs-long molecular dynamics simulations to directly characterize the rigid-body motion of a protein in different crystal forms. For ubiquitin crystals investigated in this study we determine the range of possible correlation times of rocking motion, 0.1-100 μs. The amplitude of rocking varies from one crystal form to another and is correlated with the resolution obtainable in X-ray diffraction experiments.


    Organizational Affiliation

    Institut fu¨r Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany.,Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, USA.,Université Grenoble Alpes, IBS, F-38044 Grenoble, France.,CEA, Institut de Biologie Structurale, F-38044 Grenoble, France.,CNRS, Institut de Biologie Structurale, F-38044 Grenoble, France.,ICS-6: Structural Biochemistry, Forschungszentrum Jülich, 52425 Jülich, Germany.,Laboratory of Biomolecular NMR, St. Petersburg State University, St. Petersburg 199034, Russia.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ubiquitin
A
76Homo sapiensMutation(s): 0 
Gene Names: UBB
Find proteins for P0CG47 (Homo sapiens)
Go to Gene View: UBB
Go to UniProtKB:  P0CG47
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.15 Å
  • R-Value Free: 0.171 
  • R-Value Work: 0.137 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 27.940α = 90.00
b = 43.300β = 90.00
c = 50.190γ = 90.00
Software Package:
Software NamePurpose
XSCALEdata scaling
PHASERphasing
XDSdata reduction
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-10-14
    Type: Initial release