1H87

Gadolinium derivative of tetragonal Hen Egg-White Lysozyme at 1.7 A resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.72 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.180 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Gd-Hp-Do3A, a Complex to Obtain High-Phasing-Power Heavy Atom Derivatives for Sad and MAD Experiments. Results with Tetragonal Hen Egg-White Lysozyme

Girard, E.Chantalat, L.Vicat, J.Kahn, R.

(2001) Acta Crystallogr.,Sect.D 58: 1

  • Also Cited By: 4BAD, 4BAF, 4BAL, 4BAP, 4BAR, 4BGT, 4BGU, 4BGV, 4CL3

  • PubMed Abstract: 
  • A neutral gadolinium complex, Gd-HPDO3A, is shown to be a good candidate to use to obtain heavy-atom derivatives and solve macromolecular structures using anomalous dispersion. Tetragonal crystals of a gadolinium derivative of hen egg-white lysozyme ...

    A neutral gadolinium complex, Gd-HPDO3A, is shown to be a good candidate to use to obtain heavy-atom derivatives and solve macromolecular structures using anomalous dispersion. Tetragonal crystals of a gadolinium derivative of hen egg-white lysozyme were obtained by co-crystallization using different concentrations of the complex. Diffraction data from three derivative crystals (100, 50 and 10 mM) were collected to a resolution of 1.7 A using Cu Kalpha radiation from a rotating anode. Two strong binding sites of the gadolinium complex to the protein were located from the gadolinium anomalous signal in both the 100 and 50 mM derivatives. A single site is occupied in the 10 mM derivative. Phasing using the anomalous signal at a single wavelength (SAD method) leads to an electron-density map of high quality. The structure of the 100 mM derivative has been refined. Two molecules of the gadolinium complex are close together. Both molecules are located close to tryptophan residues. Four chloride ions were found. The exceptional quality of the SAD electron-density map, only enhanced by solvent flattening, suggests that single-wavelength anomalous scattering with the Gd-HPDO3A complex may be sufficient to solve protein structures of high molecular weight by synchrotron-radiation experiments, if not by laboratory experiments.


    Related Citations: 
    • High-Pressure Protein Crystallography (Hppx): Instrumentation, Methodology and Results on Lysozyme Crystals
      Fourme, R.,Kahn, R.,Mezouar, M.,Girard, E.,Hoerentrup, C.,Prange, T.,Ascone, I.
      (2001) J.Synchrotron Radia. 8: 1149
    • Thermal Expansion of Hen-Egg-White Lysozyme. Comparison of the 1.9 Angstroms Resolution Structures of the Tetragonal Form of the Enzyme at 100K and 298K
      Young, A.C.M.,Tilton, R.F.,Dewan, J.C.
      (1994) J.Mol.Biol. 235: 302


    Organizational Affiliation

    Laboratoire de Cristallographie Macromoléculaire, Institut de Biologie Structurale J.-P. Ebel CEA-CNRS-UJF, 41 Rue Jules Horowitz, 38027 Grenoble CEDEX 01, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
LYSOZYME C
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 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
DO3
Query on DO3

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Download CCD File 
A
10-((2R)-2-HYDROXYPROPYL)-1,4,7,10-TETRAAZACYCLODODECANE 1,4,7-TRIACETIC ACID
C17 H32 N4 O7
IQUHNCOJRJBMSU-CQSZACIVSA-N
 Ligand Interaction
GD
Query on GD

Download SDF File 
Download CCD File 
A
GADOLINIUM ATOM
Gd
UIWYJDYFSGRHKR-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.72 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.180 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 77.250α = 90.00
b = 77.250β = 90.00
c = 38.660γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
CNSphasing
SCALAdata scaling
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-01-15
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance