6HU5 | pdb_00006hu5

STRUCTURE OF HEWL BY ELECTRON DIFFRACTION AND MICROFOCUS DIFFRACTION


Experimental Data Snapshot

  • Method: ELECTRON CRYSTALLOGRAPHY
  • Resolution: 2.80 Å
  • R-Value Free: 
    0.339 (Depositor), 0.300 (DCC) 
  • R-Value Work: 
    0.297 (Depositor) 
  • R-Value Observed: 
    0.299 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.3 of the entry. See complete history

Literature

Nanobeam precession-assisted 3D electron diffraction reveals a new polymorph of hen egg-white lysozyme.

Lanza, A.Margheritis, E.Mugnaioli, E.Cappello, V.Garau, G.Gemmi, M.

(2019) IUCrJ 6: 178-188

  • DOI: https://doi.org/10.1107/S2052252518017657
  • Primary Citation Related Structures: 
    6HT2, 6HU5

  • PubMed Abstract: 

    Recent advances in 3D electron diffraction have allowed the structure determination of several model proteins from submicrometric crystals, the unit-cell parameters and structures of which could be immediately validated by known models previously obtained by X-ray crystallography. Here, the first new protein structure determined by 3D electron diffraction data is presented: a previously unobserved polymorph of hen egg-white lysozyme. This form, with unit-cell parameters a = 31.9, b = 54.4, c = 71.8 Å, β = 98.8°, grows as needle-shaped submicrometric crystals simply by vapor diffusion starting from previously reported crystallization conditions. Remarkably, the data were collected using a low-dose stepwise experimental setup consisting of a precession-assisted nanobeam of ∼150 nm, which has never previously been applied for solving protein structures. The crystal structure was additionally validated using X-ray synchrotron-radiation sources by both powder diffraction and single-crystal micro-diffraction. 3D electron diffraction can be used for the structural characterization of submicrometric macromolecular crystals and is able to identify novel protein polymorphs that are hardly visible in conventional X-ray diffraction experiments. Additionally, the analysis, which was performed on both nanocrystals and microcrystals from the same crystallization drop, suggests that an integrated view from 3D electron diffraction and X-ray microfocus diffraction can be applied to obtain insights into the molecular dynamics during protein crystal growth.


  • Organizational Affiliation
    • Center for Nanotechnology Innovation@NEST, Istituto Italiano di Tecnologia, Piazza San Silvestro 12, 56127 Pisa, Italy.

Macromolecule Content 

  • Total Structure Weight: 28.77 kDa 
  • Atom Count: 1,991 
  • Modeled Residue Count: 257 
  • Deposited Residue Count: 258 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Lysozyme C
A, B
129Gallus gallusMutation(s): 0 
EC: 3.2.1.17
UniProt
Find proteins for P00698 (Gallus gallus)
Explore P00698 
Go to UniProtKB:  P00698
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00698
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON CRYSTALLOGRAPHY
  • Resolution: 2.80 Å
  • R-Value Free:  0.339 (Depositor), 0.300 (DCC) 
  • R-Value Work:  0.297 (Depositor) 
  • R-Value Observed: 0.299 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 31.849α = 90
b = 54.38β = 98.82
c = 71.788γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
XDSphasing
CCP4phasing
PHENIXrefinement
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.13

Structure Validation

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Entry History 

Deposition Data

  • Released Date: 2019-01-23 
  • Deposition Author(s): Garau, G.

Revision History  (Full details and data files)

  • Version 1.0: 2019-01-23
    Type: Initial release
  • Version 1.1: 2019-03-27
    Changes: Data collection, Database references
  • Version 1.2: 2019-07-17
    Changes: Data collection, Derived calculations
  • Version 1.3: 2024-11-13
    Changes: Data collection, Database references, Refinement description, Structure summary