4LZT

ATOMIC RESOLUTION REFINEMENT OF TRICLINIC HEW LYSOZYME AT 295K


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.95 Å
  • R-Value Free: 0.147 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Refinement of triclinic hen egg-white lysozyme at atomic resolution.

Walsh, M.A.Schneider, T.R.Sieker, L.C.Dauter, Z.Lamzin, V.S.Wilson, K.S.

(1998) Acta Crystallogr.,Sect.D 54: 522-546

  • Primary Citation of Related Structures:  3LZT
  • Also Cited By: 1HF4

  • PubMed Abstract: 
  • X-ray diffraction data have been collected at both low (120 K) and room temperature from triclinic crystals of hen egg-white lysozyme to 0.925 and 0.950 A resolution, respectively, using synchrotron radiation. Data from one crystal were sufficient fo ...

    X-ray diffraction data have been collected at both low (120 K) and room temperature from triclinic crystals of hen egg-white lysozyme to 0.925 and 0.950 A resolution, respectively, using synchrotron radiation. Data from one crystal were sufficient for the low-temperature study, whereas three crystals were required at room temperature. Refinement was carried out using the programs PROLSQ, ARP and SHELXL to give final conventional R factors of 8.98 and 10.48% for data with F > 4sigma(F) for the low- and room-temperature structures, respectively. The estimated r.m.s. coordinate error is 0.032 A for protein atoms, 0.050 A for all atoms in the low-temperature study, and 0.038 A for protein atoms and 0.049 A for all atoms in the room-temperature case, as estimated from inversion of the blocked least-squares matrix. The low-temperature study revealed that the side chains of 24 amino acids had multiple conformations. A total of 250 waters, six nitrate ions and three acetate ions, two of which were modelled with alternate orientations were located in the electron-density maps. Three sections of the main chain were modelled in alternate conformations. The room-temperature study produced a model with multiple conformations for eight side chains and a total of 139 water molecules, six nitrate but no acetate ions. The occupancies of the water molecules were refined in both structures and this step was shown to be meaningful when assessed by use of the free R factor. A detailed description and comparison of the structures is made with reference to the previously reported structure refined at 2.0 A resolution.


    Related Citations: 
    • Refinement of Triclinic Lysozyme: I. Fourier and Least-Squares Methods
      Hodsdon, J.M.,Brown, G.M.,Sieker, L.C.,Jensen, L.H.
      (1990) Acta Crystallogr.,Sect.B 46: 54
    • Refinement of Triclinic Lysozyme: II. The Method of Stereochemically Restrained Least Squares
      Ramanadham, M.,Sieker, L.C.,Jensen, L.H.
      (1990) Acta Crystallogr.,Sect.B 46: 63


    Organizational Affiliation

    European Molecular Biology Laboratory (EMBL), c/o DESY, Notkestrasse 85, D-22603 Hamburg, Germany. walsh@anl.gov




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
LYSOZYME
A
129Gallus gallusGene 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 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NO3
Query on NO3

Download SDF File 
Download CCD File 
A
NITRATE ION
N O3
NHNBFGGVMKEFGY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.95 Å
  • R-Value Free: 0.147 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 27.240α = 88.52
b = 31.870β = 108.53
c = 34.230γ = 111.89
Software Package:
Software NamePurpose
SHELXL-96phasing
SHELXL-96refinement
DENZOdata reduction
SHELXL-96model building
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1998-04-01
    Type: Initial release
  • Version 1.1: 2008-03-25
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance