1dvb

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[[Image:1dvb.gif|left|200px]]<br /><applet load="1dvb" size="350" color="white" frame="true" align="right" spinBox="true"
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[[Image:1dvb.gif|left|200px]]
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caption="1dvb, resolution 1.9&Aring;" />
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'''RUBRERYTHRIN'''<br />
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{{Structure
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|PDB= 1dvb |SIZE=350|CAPTION= <scene name='initialview01'>1dvb</scene>, resolution 1.9&Aring;
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|SITE=
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|LIGAND= <scene name='pdbligand=FE:FE+(III)+ION'>FE</scene> and <scene name='pdbligand=ZN:ZINC ION'>ZN</scene>
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|ACTIVITY=
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|GENE=
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}}
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'''RUBRERYTHRIN'''
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==Overview==
==Overview==
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==About this Structure==
==About this Structure==
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1DVB is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Desulfovibrio_vulgaris Desulfovibrio vulgaris] with <scene name='pdbligand=FE:'>FE</scene> and <scene name='pdbligand=ZN:'>ZN</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DVB OCA].
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1DVB is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Desulfovibrio_vulgaris Desulfovibrio vulgaris]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DVB OCA].
==Reference==
==Reference==
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The 1.9 A crystal structure of the "as isolated" rubrerythrin from Desulfovibrio vulgaris: some surprising results., Sieker LC, Holmes M, Le Trong I, Turley S, Liu MY, LeGall J, Stenkamp RE, J Biol Inorg Chem. 2000 Aug;5(4):505-13. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=10968622 10968622]
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The 1.9 A crystal structure of the "as isolated" rubrerythrin from Desulfovibrio vulgaris: some surprising results., Sieker LC, Holmes M, Le Trong I, Turley S, Liu MY, LeGall J, Stenkamp RE, J Biol Inorg Chem. 2000 Aug;5(4):505-13. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/10968622 10968622]
[[Category: Desulfovibrio vulgaris]]
[[Category: Desulfovibrio vulgaris]]
[[Category: Single protein]]
[[Category: Single protein]]
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[[Category: zinc]]
[[Category: zinc]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 12:20:53 2008''
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 10:44:56 2008''

Revision as of 08:44, 20 March 2008

Image:1dvb.gif


PDB ID 1dvb

Drag the structure with the mouse to rotate
, resolution 1.9Å
Ligands: and
Coordinates: save as pdb, mmCIF, xml



RUBRERYTHRIN


Overview

Rubrerythrin is a non-heme iron dimeric protein isolated from the sulfate-reducing bacterium Desulfovibrio vulgaris. Each monomer has one mononuclear iron center similar to rubredoxin and one dinuclear metal center similar to hemerythrin or ribonucleotide reductase. The 1.88 A X-ray structure of the "as isolated" molecule and a uranyl heavy atom derivative have been solved by molecular replacement techniques. The resulting model of the native "as isolated" molecule, including 164 water molecules, has been refined giving a final R factor of 0.197 (R(free) = 0.255). The structure has the same general protein fold, domain structure, and dimeric interactions as previously found for rubrerythrin [1, 2], but it also has some interesting undetected differences at the metal centers. The refined model of the protein structure has a cis peptide between residues 78 and 79. The Fe-Cys4 center has a previously undetected strong seventh N-H...S hydrogen bond in addition to the six N-H...S bonds usually found in rubredoxin. The dinuclear metal center has a hexacoordinate Fe atom and a tetracoordinate Zn atom. Each metal is coordinated by a GluXXHis polypeptide chain segment. The Zn atom binds at a site distinctly different from that found in the structure of a diiron rubrerythrin. Difference electron density for the uranyl derivative shows an extremely large peak adjacent to and replacing the Zn atom, indicating that this particular site is capable of binding other atoms. This feature/ability may give rise to some of the confusing activities ascribed to this molecule.

About this Structure

1DVB is a Single protein structure of sequence from Desulfovibrio vulgaris. Full crystallographic information is available from OCA.

Reference

The 1.9 A crystal structure of the "as isolated" rubrerythrin from Desulfovibrio vulgaris: some surprising results., Sieker LC, Holmes M, Le Trong I, Turley S, Liu MY, LeGall J, Stenkamp RE, J Biol Inorg Chem. 2000 Aug;5(4):505-13. PMID:10968622

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