1L2K

Neutron Structure Determination of Sperm Whale Met-Myoglobin at 1.5A Resolution.


Experimental Data Snapshot

  • Method: NEUTRON DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.201 

wwPDB Validation

Currently 1L2K does not have a wwPDB validation report.


This is version 1.2 of the entry. See complete history

Literature

Hydrogen and deuterium in myoglobin as seen by a neutron structure determination at 1.5 A resolution.

Ostermann, A.Tanaka, I.Engler, N.Niimura, N.Parak, F.G.

(2002) Biophys.Chem. 95: 183-193


  • PubMed Abstract: 
  • From the first days of protein neutron structure determination sperm whale myoglobin was an object under investigation [Nature 224 (1969) 143, J. Mol. Biol. 220 (1991) 381]. Nevertheless myoglobin is still of interest [Proc. Natl. Acad. Sci. USA 97 ( ...

    From the first days of protein neutron structure determination sperm whale myoglobin was an object under investigation [Nature 224 (1969) 143, J. Mol. Biol. 220 (1991) 381]. Nevertheless myoglobin is still of interest [Proc. Natl. Acad. Sci. USA 97 (2000) 3872]. The feasibility of the monochromatic neutron diffractometer BIX-3 at the JRR-3M reactor at the JAERI [J. Phys. Chem. Solids 60 (1999) 1623], to collect high-resolution diffraction data in a relatively short time stimulated us to repeat the structural determination of myoglobin. The structure of metmyoglobin has been determined up to a resolution of 1.5 A. The hydrogen atoms were replaced in part, by deuterium soaking the crystals for more than 10 years in D(2)O. A refinement of all atoms has been performed including the refinement of individual mean square displacements and occupancies of the exchangeable protons in backbone hydrogen bonds. A method is described to show clear negative scattering densities of the H atoms. Water molecules within the protein and on the molecule surface are shown. The exchangeability of H atoms is correlated with structural distribution and flexibility.


    Related Citations: 
    • Neutrons Expand the Field of Structural Biology
      Niimura, N.
      (1999) CURR.OPIN.STRUCT.BIOL. 9: 602


    Organizational Affiliation

    Advanced Science Research Centre, JAERI, Tokai-Mura, Ibaraki 319-1195, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
MYOGLOBIN
A
153Physeter catodonGene Names: MB
Find proteins for P02185 (Physeter catodon)
Go to Gene View: MB
Go to UniProtKB:  P02185
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

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Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
HEM
Query on HEM

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Download CCD File 
A
PROTOPORPHYRIN IX CONTAINING FE
HEME
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
ND4
Query on ND4

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Download CCD File 
A
AMMONIUM CATION WITH D
N
QGZKDVFQNNGYKY-JBISRTOLSA-O
 Ligand Interaction
DOD
Query on DOD

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Download CCD File 
A
DEUTERATED WATER
D2 O
XLYOFNOQVPJJNP-ZSJDYOACSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: NEUTRON DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.201 
Software Package:
Software NamePurpose
DENZOdata reduction
CNSrefinement
X-PLORmodel building
X-PLORphasing
SCALEPACKdata scaling

Structure Validation

Currently 1L2K does not have a wwPDB validation report.



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-08-21
    Type: Initial release
  • Version 1.1: 2008-04-28
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Non-polymer description, Version format compliance