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PDBsum entry 1l2k
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Oxygen storage/transport PDB id
1l2k

 

 

 

 

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Contents
Protein chain
151 a.a. *
Ligands
SO4 ×2
ND4
HEM-DOD
DOD ×73
* Residue conservation analysis
PDB id:
1l2k
Name: Oxygen storage/transport
Title: Neutron structure determination of sperm whale met-myoglobin at 1.5a resolution.
Structure: Myoglobin. Chain: a
Source: Physeter catodon. Sperm whale. Organism_taxid: 9755. Tissue: muscle
Authors: A.Ostermann,I.Tanaka,N.Engler,N.Niimura,F.G.Parak
Key ref: A.Ostermann et al. (2002). Hydrogen and deuterium in myoglobin as seen by a neutron structure determination at 1.5 A resolution. Biophys Chem, 95, 183-193. PubMed id: 12062378 DOI: 10.1016/S0301-4622(01)00255-1
Date:
21-Feb-02     Release date:   21-Aug-02    
PROCHECK
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 Headers
 References

Protein chain
Pfam   ArchSchema ?
P02185  (MYG_PHYMC) -  Myoglobin from Physeter macrocephalus
Seq:
Struc: 		154 a.a.
151 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.?
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

 

 
DOI no: 10.1016/S0301-4622(01)00255-1 Biophys Chem 95:183-193 (2002)
PubMed id: 12062378  
 
 
Hydrogen and deuterium in myoglobin as seen by a neutron structure determination at 1.5 A resolution.
A.Ostermann, I.Tanaka, N.Engler, N.Niimura, F.G.Parak.
 
  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 (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.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
20445231 A.S.Gardberg, A.R.Del Castillo, K.L.Weiss, F.Meilleur, M.P.Blakeley, and D.A.Myles (2010).
Unambiguous determination of H-atom positions: comparing results from neutron and high-resolution X-ray crystallography.
  Acta Crystallogr D Biol Crystallogr, 66, 558-567.
PDB codes: 3kyu 3kyv 3kyw 3kyx 3kyy
19690366 D.Yagi, T.Yamada, K.Kurihara, Y.Ohnishi, M.Yamashita, T.Tamada, I.Tanaka, R.Kuroki, and N.Niimura (2009).
A neutron crystallographic analysis of phosphate-free ribonuclease A at 1.7 A resolution.
  Acta Crystallogr D Biol Crystallogr, 65, 892-899.
PDB code: 3a1r
18656544 M.P.Blakeley, P.Langan, N.Niimura, and A.Podjarny (2008).
Neutron crystallography: opportunities, challenges, and limitations.
  Curr Opin Struct Biol, 18, 593-600.  
18156668 N.Niimura, and R.Bau (2008).
Neutron protein crystallography: beyond the folding structure of biological macromolecules.
  Acta Crystallogr A, 64, 12-22.  
16897039 F.Meilleur, D.A.Myles, and M.P.Blakeley (2006).
Neutron Laue macromolecular crystallography.
  Eur Biophys J, 35, 611-620.  
15858267 B.C.Bennett, F.Meilleur, D.A.Myles, E.E.Howell, and C.G.Dealwis (2005).
Preliminary neutron diffraction studies of Escherichia coli dihydrofolate reductase bound to the anticancer drug methotrexate.
  Acta Crystallogr D Biol Crystallogr, 61, 574-579.  
15858263 F.Meilleur, M.T.Dauvergne, I.Schlichting, and D.A.Myles (2005).
Production and X-ray crystallographic analysis of fully deuterated cytochrome P450cam.
  Acta Crystallogr D Biol Crystallogr, 61, 539-544.
PDB codes: 1yrc 1yrd
16239733 J.B.Artero, M.Härtlein, S.McSweeney, and P.Timmins (2005).
A comparison of refined X-ray structures of hydrogenated and perdeuterated rat gammaE-crystallin in H2O and D2O.
  Acta Crystallogr D Biol Crystallogr, 61, 1541-1549.
PDB codes: 1zgt 1zie 1ziq 1zir
16114036 L.R.Forrest, and B.Honig (2005).
An assessment of the accuracy of methods for predicting hydrogen positions in protein structures.
  Proteins, 61, 296-309.  
15756816 M.Z.Atassi, and C.Childress (2005).
Oxygen-binding heme complexes of peptides designed to mimic the heme environment of myoglobin and hemoglobin.
  Protein J, 24, 37-49.  
15914673 S.Arai, T.Chatake, T.Ohhara, K.Kurihara, I.Tanaka, N.Suzuki, Z.Fujimoto, H.Mizuno, and N.Niimura (2005).
Complicated water orientations in the minor groove of the B-DNA decamer d(CCATTAATGG)2 observed by neutron diffraction measurements.
  Nucleic Acids Res, 33, 3017-3024.
PDB codes: 1wqy 1wqz
16041074 T.Chatake, I.Tanaka, H.Umino, S.Arai, and N.Niimura (2005).
The hydration structure of a Z-DNA hexameric duplex determined by a neutron diffraction technique.
  Acta Crystallogr D Biol Crystallogr, 61, 1088-1098.
PDB codes: 1v9g 1woe
15272083 K.Kurihara, I.Tanaka, T.Chatake, M.W.Adams, F.E.Jenney, N.Moiseeva, R.Bau, and N.Niimura (2004).
Neutron crystallographic study on rubredoxin from Pyrococcus furiosus by BIX-3, a single-crystal diffractometer for biomacromolecules.
  Proc Natl Acad Sci U S A, 101, 11215-11220.
PDB code: 1vcx
14739317 M.M.Teeter (2004).
Myoglobin cavities provide interior ligand pathway.
  Protein Sci, 13, 313-318.  
15448207 P.W.Fenimore, H.Frauenfelder, B.H.McMahon, and R.D.Young (2004).
Bulk-solvent and hydration-shell fluctuations, similar to alpha- and beta-fluctuations in glasses, control protein motions and functions.
  Proc Natl Acad Sci U S A, 101, 14408-14413.  
14993708 V.U.Tuominen, D.A.Myles, M.T.Dauvergne, R.Lahti, P.Heikinheimo, and A.Goldman (2004).
Production and preliminary analysis of perdeuterated yeast inorganic pyrophosphatase crystals suitable for neutron diffraction.
  Acta Crystallogr D Biol Crystallogr, 60, 606-609.  
15057940 W.Radding, and G.N.Phillips (2004).
Kinetic proofreading by the cavity system of myoglobin: protection from poisoning.
  Bioessays, 26, 422-433.  
12937341 N.Engler, A.Ostermann, N.Niimura, and F.G.Parak (2003).
Hydrogen atoms in proteins: positions and dynamics.
  Proc Natl Acad Sci U S A, 100, 10243-10248.  
12557193 T.Chatake, A.Ostermann, K.Kurihara, F.G.Parak, and N.Niimura (2003).
Hydration in proteins observed by high-resolution neutron crystallography.
  Proteins, 50, 516-523.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.

 

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