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| | ==Conserved hypothetical protein from Pyrococcus furiosus Pfu-392566-001== | | ==Conserved hypothetical protein from Pyrococcus furiosus Pfu-392566-001== |
| - | <StructureSection load='1vk1' size='340' side='right' caption='[[1vk1]], [[Resolution|resolution]] 1.20Å' scene=''> | + | <StructureSection load='1vk1' size='340' side='right'caption='[[1vk1]], [[Resolution|resolution]] 1.20Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[1vk1]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_43587 Atcc 43587]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1VK1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1VK1 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[1vk1]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrococcus_furiosus Pyrococcus furiosus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1VK1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1VK1 FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.2Å</td></tr> |
| - | <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MLY:N-DIMETHYL-LYSINE'>MLY</scene></td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MLY:N-DIMETHYL-LYSINE'>MLY</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr> |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1vk1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1vk1 OCA], [http://pdbe.org/1vk1 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1vk1 RCSB], [http://www.ebi.ac.uk/pdbsum/1vk1 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1vk1 ProSAT], [http://www.topsan.org/Proteins/SECSG/1vk1 TOPSAN]</span></td></tr> | + | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1vk1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1vk1 OCA], [https://pdbe.org/1vk1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1vk1 RCSB], [https://www.ebi.ac.uk/pdbsum/1vk1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1vk1 ProSAT], [https://www.topsan.org/Proteins/SECSG/1vk1 TOPSAN]</span></td></tr> |
| | </table> | | </table> |
| | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/Q8U3S5_PYRFU Q8U3S5_PYRFU] |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Atcc 43587]] | + | [[Category: Large Structures]] |
| - | [[Category: Adams, M W.W]]
| + | |
| - | [[Category: Brereton, P S]]
| + | |
| - | [[Category: Chang, J]]
| + | |
| - | [[Category: Chen, L]]
| + | |
| - | [[Category: II, F L.Poole]]
| + | |
| - | [[Category: Izumi, M]]
| + | |
| - | [[Category: Jenney, F E]]
| + | |
| - | [[Category: Lee, D]]
| + | |
| - | [[Category: Liu, Z J]]
| + | |
| - | [[Category: Ng, J]]
| + | |
| - | [[Category: Richardson, D C]]
| + | |
| - | [[Category: Richardson, J S]]
| + | |
| - | [[Category: Rose, J]]
| + | |
| - | [[Category: Structural genomic]]
| + | |
| - | [[Category: Shah, A]]
| + | |
| - | [[Category: Shah, C]]
| + | |
| - | [[Category: Sugar, F J]]
| + | |
| - | [[Category: Tempel, W]]
| + | |
| - | [[Category: Wang, B C]]
| + | |
| - | [[Category: Yang, H]]
| + | |
| - | [[Category: Zhao, M]]
| + | |
| - | [[Category: Conserved hypothetical protein]]
| + | |
| - | [[Category: Dimethyl lysine]]
| + | |
| - | [[Category: PSI, Protein structure initiative]]
| + | |
| | [[Category: Pyrococcus furiosus]] | | [[Category: Pyrococcus furiosus]] |
| - | [[Category: Reductive methylation]] | + | [[Category: Adams MWW]] |
| - | [[Category: Secsg]] | + | [[Category: Brereton PS]] |
| - | [[Category: Unknown function]] | + | [[Category: Chang J]] |
| | + | [[Category: Chen L]] |
| | + | [[Category: Izumi M]] |
| | + | [[Category: Jenney Jr FE]] |
| | + | [[Category: Lee D]] |
| | + | [[Category: Liu ZJ]] |
| | + | [[Category: Ng J]] |
| | + | [[Category: Poole II FL]] |
| | + | [[Category: Richardson DC]] |
| | + | [[Category: Richardson JS]] |
| | + | [[Category: Rose J]] |
| | + | [[Category: Shah A]] |
| | + | [[Category: Shah C]] |
| | + | [[Category: Sugar FJ]] |
| | + | [[Category: Tempel W]] |
| | + | [[Category: Wang BC]] |
| | + | [[Category: Yang H]] |
| | + | [[Category: Zhao M]] |
| Structural highlights
1vk1 is a 1 chain structure with sequence from Pyrococcus furiosus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
| | Method: | X-ray diffraction, Resolution 1.2Å |
| Ligands: | , , , |
| Resources: | FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT, TOPSAN |
Function
Q8U3S5_PYRFU
Evolutionary Conservation
Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.
Publication Abstract from PubMed
BACKGROUND: The major bottleneck for determination of 3 D structures of proteins using X-rays is the production of diffraction quality crystals. Often proteins are subjected to chemical modification to improve the chances of crystallization RESULTS: Here, we report the successful crystallization of a nuclease employing a reductive methylation protocol. The key to crystallization was the successful introduction of 44 new cohesive (NZ) CH...O contacts (3.2-3.7 A) by the addition of 2 methyl groups to the side chain amine nitrogen (NZ) of 9 lysine residues of the nuclease. The new contacts dramatically altered the crystallization properties of the protein, resulting in crystals that diffracted to 1.2 A resolution. Analytical ultracentrifugation analysis and thermodynamics results revealed a more compact protein structure with better solvent exclusion of buried Trp residues in the folded state of the methylated protein, assisting crystallization. CONCLUSION: In this study, introduction of novel cohesive (NZ)CH...O contacts by reductive methylation resulted in the crystallization of a protein that had previously resisted crystallization in spite of extensive purification and crystallization space screening. Introduction of (NZ)CH...O contacts could provide a solution to crystallization problems for a broad range of protein targets.
(NZ)CH...O contacts assist crystallization of a ParB-like nuclease.,Shaw N, Cheng C, Tempel W, Chang J, Ng J, Wang XY, Perrett S, Rose J, Rao Z, Wang BC, Liu ZJ BMC Struct Biol. 2007 Jul 7;7:46. PMID:17617922[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Shaw N, Cheng C, Tempel W, Chang J, Ng J, Wang XY, Perrett S, Rose J, Rao Z, Wang BC, Liu ZJ. (NZ)CH...O contacts assist crystallization of a ParB-like nuclease. BMC Struct Biol. 2007 Jul 7;7:46. PMID:17617922 doi:http://dx.doi.org/10.1186/1472-6807-7-46
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