5VNR

X-ray strucutre of perdeuterated T4 lysozyme cysteine-free pseudo-wild type at cryogenic temperature


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.631 Å
  • R-Value Free: 0.186 
  • R-Value Work: 0.158 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Neutron crystallographic studies of T4 lysozyme at cryogenic temperature.

Li, L.Shukla, S.Meilleur, F.Standaert, R.F.Pierce, J.Myles, D.A.A.Cuneo, M.J.

(2017) Protein Sci. 26: 2098-2104

  • DOI: 10.1002/pro.3231
  • Primary Citation of Related Structures:  5VNQ

  • PubMed Abstract: 
  • Bacteriophage T4 lysozyme (T4L) has been used as a paradigm for seminal biophysical studies on protein structure, dynamics, and stability. Approximately 700 mutants of this protein and their respective complexes have been characterized by X-ray cryst ...

    Bacteriophage T4 lysozyme (T4L) has been used as a paradigm for seminal biophysical studies on protein structure, dynamics, and stability. Approximately 700 mutants of this protein and their respective complexes have been characterized by X-ray crystallography; however, despite the high resolution diffraction limits attained in several studies, no hydrogen atoms were reported being visualized in the electron density maps. To address this, a 2.2 Å-resolution neutron data set was collected at 80 K from a crystal of perdeuterated T4L pseudo-wild type. We describe a near complete atomic structure of T4L, which includes the positions of 1737 hydrogen atoms determined by neutron crystallography. The cryogenic neutron model reveals explicit detail of the hydrogen bonding interactions in the protein, in addition to the protonation states of several important residues.


    Organizational Affiliation

    Oak Ridge National Laboratory, Neutron Sciences Directorate, Oak Ridge, Tennessee, 37831.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Endolysin
A
164Enterobacteria phage T4Gene Names: E
EC: 3.2.1.17
Find proteins for P00720 (Enterobacteria phage T4)
Go to UniProtKB:  P00720
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

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A
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
NA
Query on NA

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A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

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A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
GOL
Query on GOL

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A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
HED
Query on HED

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A
2-HYDROXYETHYL DISULFIDE
C4 H10 O2 S2
KYNFOMQIXZUKRK-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.631 Å
  • R-Value Free: 0.186 
  • R-Value Work: 0.158 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 59.830α = 90.00
b = 59.830β = 90.00
c = 95.461γ = 120.00
Software Package:
Software NamePurpose
PHENIXrefinement
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-07-26
    Type: Initial release
  • Version 1.1: 2017-10-04
    Type: Database references