2j8d
From Proteopedia
(Difference between revisions)
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<StructureSection load='2j8d' size='340' side='right' caption='[[2j8d]], [[Resolution|resolution]] 2.07Å' scene=''> | <StructureSection load='2j8d' size='340' side='right' caption='[[2j8d]], [[Resolution|resolution]] 2.07Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
| - | [[2j8d]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Rhodobacter_sphaeroides Rhodobacter sphaeroides]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2J8D OCA]. <br> | + | <table><tr><td colspan='2'>[[2j8d]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Rhodobacter_sphaeroides Rhodobacter sphaeroides]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2J8D OCA]. <br> |
| - | <b>[[Ligand|Ligands:]]</b> <scene name='pdbligand=BCL:BACTERIOCHLOROPHYLL+A'>BCL</scene>, <scene name='pdbligand=BPH:BACTERIOPHEOPHYTIN+A'>BPH</scene>, <scene name='pdbligand=CDL:CARDIOLIPIN'>CDL</scene>, <scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=HTO:HEPTANE-1,2,3-TRIOL'>HTO</scene>, <scene name='pdbligand=LDA:LAURYL+DIMETHYLAMINE-N-OXIDE'>LDA</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=SPO:SPHEROIDENE'>SPO</scene>, <scene name='pdbligand=U10:UBIQUINONE-10'>U10</scene><br> | + | </td></tr><tr><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BCL:BACTERIOCHLOROPHYLL+A'>BCL</scene>, <scene name='pdbligand=BPH:BACTERIOPHEOPHYTIN+A'>BPH</scene>, <scene name='pdbligand=CDL:CARDIOLIPIN'>CDL</scene>, <scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=HTO:HEPTANE-1,2,3-TRIOL'>HTO</scene>, <scene name='pdbligand=LDA:LAURYL+DIMETHYLAMINE-N-OXIDE'>LDA</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=SPO:SPHEROIDENE'>SPO</scene>, <scene name='pdbligand=U10:UBIQUINONE-10'>U10</scene><br> |
| - | <b>[[Related_structure|Related:]]</b> [[1aig|1aig]], [[1aij|1aij]], [[1ds8|1ds8]], [[1dv3|1dv3]], [[1dv6|1dv6]], [[1e14|1e14]], [[1e6d|1e6d]], [[1f6n|1f6n]], [[1fnp|1fnp]], [[1fnq|1fnq]], [[1jgw|1jgw]], [[1jgx|1jgx]], [[1jgy|1jgy]], [[1jgz|1jgz]], [[1jh0|1jh0]], [[1k6l|1k6l]], [[1k6n|1k6n]], [[1kby|1kby]], [[1l9b|1l9b]], [[1l9j|1l9j]], [[1m3x|1m3x]], [[1mps|1mps]], [[1ogv|1ogv]], [[1pcr|1pcr]], [[1pss|1pss]], [[1pst|1pst]], [[1qov|1qov]], [[1rg5|1rg5]], [[1rgn|1rgn]], [[1rqk|1rqk]], [[1rvj|1rvj]], [[1ry5|1ry5]], [[1rzh|1rzh]], [[1rzz|1rzz]], [[1s00|1s00]], [[1umx|1umx]], [[1yst|1yst]], [[1z9j|1z9j]], [[1z9k|1z9k]], [[2bnp|2bnp]], [[2bns|2bns]], [[2boz|2boz]], [[2j8c|2j8c]], [[2rcr|2rcr]], [[4rcr|4rcr]]< | + | <tr><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1aig|1aig]], [[1aij|1aij]], [[1ds8|1ds8]], [[1dv3|1dv3]], [[1dv6|1dv6]], [[1e14|1e14]], [[1e6d|1e6d]], [[1f6n|1f6n]], [[1fnp|1fnp]], [[1fnq|1fnq]], [[1jgw|1jgw]], [[1jgx|1jgx]], [[1jgy|1jgy]], [[1jgz|1jgz]], [[1jh0|1jh0]], [[1k6l|1k6l]], [[1k6n|1k6n]], [[1kby|1kby]], [[1l9b|1l9b]], [[1l9j|1l9j]], [[1m3x|1m3x]], [[1mps|1mps]], [[1ogv|1ogv]], [[1pcr|1pcr]], [[1pss|1pss]], [[1pst|1pst]], [[1qov|1qov]], [[1rg5|1rg5]], [[1rgn|1rgn]], [[1rqk|1rqk]], [[1rvj|1rvj]], [[1ry5|1ry5]], [[1rzh|1rzh]], [[1rzz|1rzz]], [[1s00|1s00]], [[1umx|1umx]], [[1yst|1yst]], [[1z9j|1z9j]], [[1z9k|1z9k]], [[2bnp|2bnp]], [[2bns|2bns]], [[2boz|2boz]], [[2j8c|2j8c]], [[2rcr|2rcr]], [[4rcr|4rcr]]</td></tr> |
| - | <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>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> |
| - | <b>Resources:</b> <span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2j8d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2j8d OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2j8d RCSB], [http://www.ebi.ac.uk/pdbsum/2j8d PDBsum]</span>< | + | <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=2j8d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2j8d OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2j8d RCSB], [http://www.ebi.ac.uk/pdbsum/2j8d 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 structure of the photosynthetic reaction-center from Rhodobacter sphaeroides has been determined at four different pH values (6.5, 8.0, 9.0, 10.0) in the neutral and in charge separated states. At pH 8.0, in the neutral state, we obtain a resolution of 1.87 A, which is the best ever reported for the bacterial reaction center protein. Our crystallographic data confirm the existence of two different binding positions of the secondary quinone (QB). We observe a new orientation of QB in its distal position, which shows no ring-flip compared to the orientation in the proximal position. Datasets collected for the different pH values show a pH-dependence of the population of the proximal position. The new orientation of QB in the distal position and the pH-dependence could be confirmed by continuum electrostatics calculations. Our calculations are in agreement with the experimentally observed proton uptake upon charge separation. The high resolution of our crystallographic data allows us to identify new water molecules and external residues being involved in two previously described hydrogen bond proton channels. These extended proton-transfer pathways, ending at either of the two oxo-groups of QB in its proximal position, provide additional evidence that ring-flipping is not required for complete protonation of QB upon reduction. | The structure of the photosynthetic reaction-center from Rhodobacter sphaeroides has been determined at four different pH values (6.5, 8.0, 9.0, 10.0) in the neutral and in charge separated states. At pH 8.0, in the neutral state, we obtain a resolution of 1.87 A, which is the best ever reported for the bacterial reaction center protein. Our crystallographic data confirm the existence of two different binding positions of the secondary quinone (QB). We observe a new orientation of QB in its distal position, which shows no ring-flip compared to the orientation in the proximal position. Datasets collected for the different pH values show a pH-dependence of the population of the proximal position. The new orientation of QB in the distal position and the pH-dependence could be confirmed by continuum electrostatics calculations. Our calculations are in agreement with the experimentally observed proton uptake upon charge separation. The high resolution of our crystallographic data allows us to identify new water molecules and external residues being involved in two previously described hydrogen bond proton channels. These extended proton-transfer pathways, ending at either of the two oxo-groups of QB in its proximal position, provide additional evidence that ring-flipping is not required for complete protonation of QB upon reduction. | ||
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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 10:02, 1 May 2014
X-RAY HIGH RESOLUTION STRUCTURE OF THE PHOTOSYNTHETIC REACTION CENTER FROM RB. SPHAEROIDES AT PH 8 IN THE CHARGE-SEPARATED STATE
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Categories: Rhodobacter sphaeroides | Diehm, R. | Fritzsch, G. | Koepke, J. | Bacteriochlorophyll | Binding positions of the secondary quinone qb | Cardiolipin | Chlorophyll | Chromophore | Electron transport | Glucosylgalactosyl diacylglycerol | Iron | Magnesium | Membrane | Metal-binding | Phosphatidylcholine | Photosynthesis | Proton translocation pathway | Reaction center | Transmembrane | Transport
