Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 8.58 kDa 
• Atom Count: 788 
• Modelled Residue Count: 72 
• Deposited Residue Count: 76 
• Unique protein chains: 1

4XOF

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

• PDB DOI: 10.2210/pdb4XOF/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2015-01-16 Released: 2015-10-14 
• Deposition Author(s): Coquelle, N., Ma, P., Schanda, P., Colletier, J.P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.15 Å
• R-Value Free: 0.171 
• R-Value Work: 0.137 
• R-Value Observed: 0.139 

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

• PubMed: 26436197 
• DOI: 10.1038/ncomms9361
• Primary Citation of Related Structures:  
  4XOF, 4XOK, 4XOL


• 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. 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.

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Organizational Affiliation: 

CNRS, Institut de Biologie Structurale, F-38044 Grenoble, France.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin	A	76	Homo sapiens	Mutation(s): 0  Gene Names: UBB
UniProt & NIH Common Fund Data Resources
Find proteins for P0CG47 (Homo sapiens) Explore P0CG47  Go to UniProtKB:  P0CG47
PHAROS:  P0CG47

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.15 Å
• R-Value Free: 0.171 
• R-Value Work: 0.137 
• R-Value Observed: 0.139 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 27.94	α = 90
b = 43.3	β = 90
c = 50.19	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2015-01-16 
• Released Date: 2015-10-14 
Deposition Author(s): Coquelle, N., Ma, P., Schanda, P., Colletier, J.P.

Revision History  

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