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| - | [[Image:1ovu.jpg|left|200px]] | |
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| - | {{Structure
| + | ==CRYSTAL STRUCTURE OF FOUR-HELIX BUNDLE MODEL di-Co(II)-DF1-L13A (form I)== |
| - | |PDB= 1ovu |SIZE=350|CAPTION= <scene name='initialview01'>1ovu</scene>, resolution 3.10Å
| + | <StructureSection load='1ovu' size='340' side='right'caption='[[1ovu]], [[Resolution|resolution]] 3.10Å' scene=''> |
| - | |SITE=
| + | == Structural highlights == |
| - | |LIGAND= <scene name='pdbligand=ACE:ACETYL+GROUP'>ACE</scene>, <scene name='pdbligand=CO:COBALT+(II)+ION'>CO</scene>, <scene name='pdbligand=NH2:AMINO+GROUP'>NH2</scene> | + | <table><tr><td colspan='2'>[[1ovu]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1OVU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1OVU FirstGlance]. <br> |
| - | |ACTIVITY=
| + | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACE:ACETYL+GROUP'>ACE</scene>, <scene name='pdbligand=CO:COBALT+(II)+ION'>CO</scene>, <scene name='pdbligand=NH2:AMINO+GROUP'>NH2</scene></td></tr> |
| - | |GENE=
| + | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1ovu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ovu OCA], [https://pdbe.org/1ovu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ovu RCSB], [https://www.ebi.ac.uk/pdbsum/1ovu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ovu ProSAT]</span></td></tr> |
| - | |DOMAIN=
| + | </table> |
| - | |RELATEDENTRY=[[1ec5|1ec5]], [[1jm0|1jm0]], [[1jmb|1jmb]], [[1lt1|1lt1]], [[1ovr|1OVR]], [[1ovv|1OVV]]
| + | <div style="background-color:#fffaf0;"> |
| - | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1ovu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ovu OCA], [http://www.ebi.ac.uk/pdbsum/1ovu PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1ovu RCSB]</span>
| + | == Publication Abstract from PubMed == |
| - | }}
| + | The de novo protein DF1 is a minimal model for diiron and dimanganese metalloproteins, such as soluble methane monooxygenase. DF1 is a homodimeric four-helix bundle whose dinuclear center is formed by two bridging Glu side chains, two chelating Glu side chains, and two monodentate His ligands. Here, we report the di-Mn(II) and di-Co(II) derivatives of variants of this protein. Together with previously solved structures, 23 crystallographically independent four-helix bundle structures of DF1 variants have been determined, which differ in the bound metal ions and size of the active site cavity. For the di-Mn(II) derivatives, as the size of the cavity increases, the number and polarity of exogenous ligands increases. This collection of structures was analyzed to determine the relationship between protein conformation and the geometry of the active site. The primary mode of backbone movement involves a coordinated tilting and sliding of the first helix in the helix-loop-helix motif. Sliding depends on crystal-packing forces, the steric bulk of a critical residue that determines the dimensions of the active site access cavity, and the intermetal distance. Additionally, a torsional motion of the bridging carboxylates modulates the intermetal distance. This analysis provides a critical evaluation of how conformation, flexibility, and active site accessibility affect the geometry and ligand-binding properties of a metal center. The geometric parameters defining the DF structures were compared to natural diiron proteins; DF proteins have a restricted active site cavity, which may have implications for substrate recognition and chemical stability. |
| | | | |
| - | '''CRYSTAL STRUCTURE OF FOUR-HELIX BUNDLE MODEL di-Co(II)-DF1-L13A (form I)'''
| + | Response of a designed metalloprotein to changes in metal ion coordination, exogenous ligands, and active site volume determined by X-ray crystallography.,Geremia S, Di Costanzo L, Randaccio L, Engel DE, Lombardi A, Nastri F, DeGrado WF J Am Chem Soc. 2005 Dec 14;127(49):17266-76. PMID:16332076<ref>PMID:16332076</ref> |
| | | | |
| - | | + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> |
| - | ==Overview==
| + | </div> |
| - | Diffraction data from two non-isomorphous crystals (forms 1 and 2) of an artificial protein with a four-helix bundle motif, di-Co(II)-DF1-L13A, have been collected using synchrotron radiation. The phase of form 1 has been assigned using the group and minimal non-isomorphic supergroup relation between the space group of the previously determined di-Mn(II)-DF1-L13G structure and the space group of this form. This unconventional method of solving the phase problem has also been tested with form 2 using a reverse relation. The structure of the latter form has been solved using the group and maximal non-isomorphic subgroup relation with the space group of form 2 of the analogous dimanganese protein. This application has shown that this phasing method can be used for solving the protein structures of polymorphic crystals as an alternative to the molecular-replacement method.
| + | <div class="pdbe-citations 1ovu" style="background-color:#fffaf0;"></div> |
| - | | + | == References == |
| - | ==About this Structure== | + | <references/> |
| - | 1OVU is a [[Protein complex]] structure of sequences from [http://en.wikipedia.org/wiki/ ]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1OVU OCA].
| + | __TOC__ |
| - | | + | </StructureSection> |
| - | ==Reference== | + | [[Category: Large Structures]] |
| - | Phasing protein structures using the group-subgroup relation., Di Costanzo L, Forneris F, Geremia S, Randaccio L, Acta Crystallogr D Biol Crystallogr. 2003 Aug;59(Pt 8):1435-9. Epub 2003, Jul 23. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/12876346 12876346]
| + | [[Category: Di Costanzo L]] |
| - | [[Category: Protein complex]] | + | [[Category: Geremia S]] |
| - | [[Category: Costanzo, L Di.]] | + | |
| - | [[Category: Geremia, S.]] | + | |
| - | [[Category: alpha-helical bundle]]
| + | |
| - | [[Category: protein design]]
| + | |
| - | | + | |
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 22:51:05 2008''
| + | |
| Structural highlights
Publication Abstract from PubMed
The de novo protein DF1 is a minimal model for diiron and dimanganese metalloproteins, such as soluble methane monooxygenase. DF1 is a homodimeric four-helix bundle whose dinuclear center is formed by two bridging Glu side chains, two chelating Glu side chains, and two monodentate His ligands. Here, we report the di-Mn(II) and di-Co(II) derivatives of variants of this protein. Together with previously solved structures, 23 crystallographically independent four-helix bundle structures of DF1 variants have been determined, which differ in the bound metal ions and size of the active site cavity. For the di-Mn(II) derivatives, as the size of the cavity increases, the number and polarity of exogenous ligands increases. This collection of structures was analyzed to determine the relationship between protein conformation and the geometry of the active site. The primary mode of backbone movement involves a coordinated tilting and sliding of the first helix in the helix-loop-helix motif. Sliding depends on crystal-packing forces, the steric bulk of a critical residue that determines the dimensions of the active site access cavity, and the intermetal distance. Additionally, a torsional motion of the bridging carboxylates modulates the intermetal distance. This analysis provides a critical evaluation of how conformation, flexibility, and active site accessibility affect the geometry and ligand-binding properties of a metal center. The geometric parameters defining the DF structures were compared to natural diiron proteins; DF proteins have a restricted active site cavity, which may have implications for substrate recognition and chemical stability.
Response of a designed metalloprotein to changes in metal ion coordination, exogenous ligands, and active site volume determined by X-ray crystallography.,Geremia S, Di Costanzo L, Randaccio L, Engel DE, Lombardi A, Nastri F, DeGrado WF J Am Chem Soc. 2005 Dec 14;127(49):17266-76. PMID:16332076[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Geremia S, Di Costanzo L, Randaccio L, Engel DE, Lombardi A, Nastri F, DeGrado WF. Response of a designed metalloprotein to changes in metal ion coordination, exogenous ligands, and active site volume determined by X-ray crystallography. J Am Chem Soc. 2005 Dec 14;127(49):17266-76. PMID:16332076 doi:10.1021/ja054199x
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