3WUL

Crystal structure of hen egg-white lysozyme


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.207 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Grease matrix as a versatile carrier of proteins for serial crystallography

Sugahara, M.Mizohata, E.Nango, E.Suzuki, M.Tanaka, T.Masuda, T.Tanaka, R.Shimamura, T.Tanaka, Y.Suno, C.Ihara, K.Pan, D.Kakinouchi, K.Sugiyama, S.Murata, M.Inoue, T.Tono, K.Song, C.Park, J.Kameshima, T.Hatsui, T.Joti, Y.Yabashi, M.Iwata, S.

(2015) Nat.Methods 12: 61-63

  • DOI: 10.1038/nmeth.3172
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Serial femtosecond X-ray crystallography (SFX) has revolutionized atomic-resolution structural investigation by expanding applicability to micrometer-sized protein crystals, even at room temperature, and by enabling dynamics studies. However, reliabl ...

    Serial femtosecond X-ray crystallography (SFX) has revolutionized atomic-resolution structural investigation by expanding applicability to micrometer-sized protein crystals, even at room temperature, and by enabling dynamics studies. However, reliable crystal-carrying media for SFX are lacking. Here we introduce a grease-matrix carrier for protein microcrystals and obtain the structures of lysozyme, glucose isomerase, thaumatin and fatty acid-binding protein type 3 under ambient conditions at a resolution of or finer than 2 Å.


    Organizational Affiliation

    Department of Applied Chemistry, Graduate School of Engineering, Osaka University, Suita, Japan.,RIKEN SPring-8 Center, Sayo, Japan.,Department of Structural Biology, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo, Japan.,1] RIKEN SPring-8 Center, Sayo, Japan. [2] Department of Cell Biology, Graduate School of Medicine, Kyoto University, Sakyo, Japan.,1] RIKEN SPring-8 Center, Sayo, Japan. [2] Laboratory of Supramolecular Crystallography, Research Center for Structural and Functional Proteomics, Institute for Protein Research, Osaka University, Suita, Japan.,Japan Synchrotron Radiation Research Institute, Sayo, Japan.,Department of Cell Biology, Graduate School of Medicine, Kyoto University, Sakyo, Japan.,Japan Science and Technology Agency (JST)-Exploratory Research for Advanced Technology (ERATO), Lipid Active Structure Project, Toyonaka, Japan.,1] RIKEN SPring-8 Center, Sayo, Japan. [2] Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Uji, Japan.




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 Gene View: LYZ
Go to UniProtKB:  P00698
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download SDF File 
Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.207 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 79.000α = 90.00
b = 79.000β = 90.00
c = 38.000γ = 90.00
Software Package:
Software NamePurpose
CrystFELdata collection
XDSdata scaling
CrystFELdata reduction
REFMACphasing
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-11-05
    Type: Initial release
  • Version 1.1: 2015-02-04
    Type: Database references
  • Version 1.2: 2018-01-24
    Type: Data collection, Refinement description