6O2H

Hen lysozyme in triclinic space group at ambient temperature - diffuse scattering dataset

  • Classification: HYDROLASE
  • Organism(s): Gallus gallus
  • Mutation(s): No 

  • Deposited: 2019-02-22 Released: 2020-02-26 
  • Deposition Author(s): Meisburger, S.P., Ando, N.
  • Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Science Foundation (NSF, United States)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.21 Å
  • R-Value Free: 0.117 
  • R-Value Work: 0.097 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Diffuse X-ray scattering from correlated motions in a protein crystal.

Meisburger, S.P.Case, D.A.Ando, N.

(2020) Nat Commun 11: 1271-1271

  • DOI: 10.1038/s41467-020-14933-6
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Protein dynamics are integral to biological function, yet few techniques are sensitive to collective atomic motions. A long-standing goal of X-ray crystallography has been to combine structural information from Bragg diffraction with dynamic informat ...

    Protein dynamics are integral to biological function, yet few techniques are sensitive to collective atomic motions. A long-standing goal of X-ray crystallography has been to combine structural information from Bragg diffraction with dynamic information contained in the diffuse scattering background. However, the origin of macromolecular diffuse scattering has been poorly understood, limiting its applicability. We present a finely sampled diffuse scattering map from triclinic lysozyme with unprecedented accuracy and detail, clearly resolving both the inter- and intramolecular correlations. These correlations are studied theoretically using both all-atom molecular dynamics and simple vibrational models. Although lattice dynamics reproduce most of the diffuse pattern, protein internal dynamics, which include hinge-bending motions, are needed to explain the short-ranged correlations revealed by Patterson analysis. These insights lay the groundwork for animating crystal structures with biochemically relevant motions.


    Organizational Affiliation

    Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, 14850, USA. nozomi.ando@cornell.edu.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Lysozyme C
A
129Gallus gallusMutation(s): 0 
Gene Names: LYZ
EC: 3.2.1.17
Find proteins for P00698 (Gallus gallus)
Go to UniProtKB:  P00698
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NO3
Query on NO3

Download CCD File 
A
NITRATE ION
N O3
NHNBFGGVMKEFGY-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.21 Å
  • R-Value Free: 0.117 
  • R-Value Work: 0.097 
  • Space Group: P 1
  • Diffraction Data DOI: 10.15785/SBGRID/747 SBGrid
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 27.424α = 88.657
b = 32.134β = 108.46
c = 34.513γ = 111.877
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
Cootmodel building

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM117757
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM100008
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM124847
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM103485
National Science Foundation (NSF, United States)United StatesDMR-1332208

Revision History 

  • Version 1.0: 2020-02-26
    Type: Initial release
  • Version 1.1: 2020-03-04
    Changes: Database references
  • Version 1.2: 2020-03-25
    Changes: Database references