2ipi
From Proteopedia
(Difference between revisions)
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<StructureSection load='2ipi' size='340' side='right' caption='[[2ipi]], [[Resolution|resolution]] 1.65Å' scene=''> | <StructureSection load='2ipi' size='340' side='right' caption='[[2ipi]], [[Resolution|resolution]] 1.65Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
| - | [[2ipi]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Streptomyces_galilaeus Streptomyces galilaeus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2IPI OCA]. <br> | + | <table><tr><td colspan='2'>[[2ipi]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Streptomyces_galilaeus Streptomyces galilaeus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2IPI OCA]. <br> |
| - | <b>[[Ligand|Ligands:]]</b> <scene name='pdbligand=AKY:METHYL+(2S,4R)-2-ETHYL-2,5,7-TRIHYDROXY-6,11-DIOXO-4-{[2,3,6-TRIDEOXY-4-O-{2,6-DIDEOXY-4-O-[(2S,6S)-6-METHYL-5-OXOTETRAHYDRO-2H-PYRAN-2-YL]-ALPHA-D-LYXO-HEXOPYRANOSYL}-3-(DIMETHYLAMINO)-D-RIBO-HEXOPYRANOSYL]OXY}-1,2,3,4,6,11-HEXAHYDROTETRACENE-1-CARBOXYLATE'>AKY</scene>, <scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene><br> | + | </td></tr><tr><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AKY:METHYL+(2S,4R)-2-ETHYL-2,5,7-TRIHYDROXY-6,11-DIOXO-4-{[2,3,6-TRIDEOXY-4-O-{2,6-DIDEOXY-4-O-[(2S,6S)-6-METHYL-5-OXOTETRAHYDRO-2H-PYRAN-2-YL]-ALPHA-D-LYXO-HEXOPYRANOSYL}-3-(DIMETHYLAMINO)-D-RIBO-HEXOPYRANOSYL]OXY}-1,2,3,4,6,11-HEXAHYDROTETRACENE-1-CARBOXYLATE'>AKY</scene>, <scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene><br> |
| - | <b>Activity:</b> <span class='plainlinks'>[http://en.wikipedia.org/wiki/Glucokinase Glucokinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.2 2.7.1.2] </span>< | + | <tr><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">AknOx ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=33899 Streptomyces galilaeus])</td></tr> |
| - | <b>Resources:</b> <span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2ipi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ipi OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2ipi RCSB], [http://www.ebi.ac.uk/pdbsum/2ipi PDBsum]</span>< | + | <tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Glucokinase Glucokinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.2 2.7.1.2] </span></td></tr> |
| + | <tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2ipi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ipi OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2ipi RCSB], [http://www.ebi.ac.uk/pdbsum/2ipi PDBsum]</span></td></tr> | ||
| + | <table> | ||
== Evolutionary Conservation == | == Evolutionary Conservation == | ||
| - | [[Image:Consurf_key_small.gif|right]] | + | [[Image:Consurf_key_small.gif|200px|right]] |
Check<jmol> | Check<jmol> | ||
<jmolCheckbox> | <jmolCheckbox> | ||
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</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf]. | </jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf]. | ||
<div style="clear:both"></div> | <div style="clear:both"></div> | ||
| + | <div style="background-color:#fffaf0;"> | ||
== Publication Abstract from PubMed == | == Publication Abstract from PubMed == | ||
The crystal structure of aclacinomycin oxidoreductase (AknOx), a tailoring enzyme involved in the biosynthesis of the polyketide antibiotic aclacinomycin, was determined to 1.65 A resolution by multiwavelength anomalous diffraction using data from selenomethionine-substituted crystals. The crystals belong to space group P2(1), with unit-cell parameters a = 68.2, b = 264.5, c = 68.2 A, beta = 119 degrees . Analysis of the intensity statistics clearly showed the presence of pseudomerohedral twinning. The data set could also be indexed and scaled with an R(sym) of 0.072 in the orthorhombic space group C222(1) (unit-cell parameters a = 69.7, b = 117.5, c = 264.4 A), indicating the possibility of pseudomerohedral twinning along the diagonal between the monoclinic a and c directions. Refinement using this twin operator resulted in an R(free) of 24.2%. A monoclinic lattice with a = c and beta close to 120 degrees can emulate a hexagonal metric, with the possibility of a threefold twin operator along the b axis and three twin domains. Refinement assuming three-domain twinning gave a final R(free) of 26.5%. The structure of AknOx can be thus refined with comparable R(free) values using either of the twin operators separately, suggesting the possibility that crystals of AknOx contain six twin domains generated by the twofold and threefold twin operators perpendicular to each other. Both twin operators coincide with noncrystallographic symmetry axes that may promote twinning. | The crystal structure of aclacinomycin oxidoreductase (AknOx), a tailoring enzyme involved in the biosynthesis of the polyketide antibiotic aclacinomycin, was determined to 1.65 A resolution by multiwavelength anomalous diffraction using data from selenomethionine-substituted crystals. The crystals belong to space group P2(1), with unit-cell parameters a = 68.2, b = 264.5, c = 68.2 A, beta = 119 degrees . Analysis of the intensity statistics clearly showed the presence of pseudomerohedral twinning. The data set could also be indexed and scaled with an R(sym) of 0.072 in the orthorhombic space group C222(1) (unit-cell parameters a = 69.7, b = 117.5, c = 264.4 A), indicating the possibility of pseudomerohedral twinning along the diagonal between the monoclinic a and c directions. Refinement using this twin operator resulted in an R(free) of 24.2%. A monoclinic lattice with a = c and beta close to 120 degrees can emulate a hexagonal metric, with the possibility of a threefold twin operator along the b axis and three twin domains. Refinement assuming three-domain twinning gave a final R(free) of 26.5%. The structure of AknOx can be thus refined with comparable R(free) values using either of the twin operators separately, suggesting the possibility that crystals of AknOx contain six twin domains generated by the twofold and threefold twin operators perpendicular to each other. Both twin operators coincide with noncrystallographic symmetry axes that may promote twinning. | ||
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From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | ||
| + | </div> | ||
== References == | == References == | ||
<references/> | <references/> | ||
Revision as of 09:52, 1 May 2014
Crystal Structure of Aclacinomycin Oxidoreductase
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