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| | ==Improving the Accuracy of Macromolecular Structure Refinement at 7 A Resolution== | | ==Improving the Accuracy of Macromolecular Structure Refinement at 7 A Resolution== |
| - | <StructureSection load='4fe1' size='340' side='right' caption='[[4fe1]], [[Resolution|resolution]] 4.92Å' scene=''> | + | <StructureSection load='4fe1' size='340' side='right'caption='[[4fe1]], [[Resolution|resolution]] 4.92Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[4fe1]] is a 12 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermosynechococcus_elongatus Thermosynechococcus elongatus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4FE1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4FE1 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[4fe1]] is a 10 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermosynechococcus_vestitus_BP-1 Thermosynechococcus vestitus BP-1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4FE1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4FE1 FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BCR:BETA-CAROTENE'>BCR</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CLA:CHLOROPHYLL+A'>CLA</scene>, <scene name='pdbligand=LHG:1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE'>LHG</scene>, <scene name='pdbligand=LMG:1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE'>LMG</scene>, <scene name='pdbligand=PQN:PHYLLOQUINONE'>PQN</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</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]] 4.9228Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1jb0|1jb0]], [[3pcq|3pcq]], [[3lw5|3lw5]]</td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BCR:BETA-CAROTENE'>BCR</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CLA:CHLOROPHYLL+A'>CLA</scene>, <scene name='pdbligand=LHG:1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE'>LHG</scene>, <scene name='pdbligand=LMG:1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE'>LMG</scene>, <scene name='pdbligand=PQN:PHYLLOQUINONE'>PQN</scene></td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Photosystem_I Photosystem I], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.97.1.12 1.97.1.12] </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=4fe1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4fe1 OCA], [https://pdbe.org/4fe1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4fe1 RCSB], [https://www.ebi.ac.uk/pdbsum/4fe1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4fe1 ProSAT]</span></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=4fe1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4fe1 OCA], [http://pdbe.org/4fe1 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4fe1 RCSB], [http://www.ebi.ac.uk/pdbsum/4fe1 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4fe1 ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/PSAF_THEEB PSAF_THEEB]] Probably participates in efficiency of electron transfer from plastocyanin to P700 (or cytochrome c553 in algae and cyanobacteria). This plastocyanin-docking protein contributes to the specific association of plastocyanin to PSI (By similarity). [[http://www.uniprot.org/uniprot/PSAC_THEEB PSAC_THEEB]] Apoprotein for the two 4Fe-4S centers FA and FB of photosystem I (PSI); essential for photochemical activity. FB is the terminal electron acceptor of PSI, donating electrons to ferredoxin. The C-terminus interacts with PsaA/B/D and helps assemble the protein into the PSI complex. Required for binding of PsaD and PsaE to PSI. PSI is a plastocyanin/cytochrome c6-ferredoxin oxidoreductase, converting photonic excitation into a charge separation, which transfers an electron from the donor P700 chlorophyll pair to the spectroscopically characterized acceptors A0, A1, FX, FA and FB in turn. [[http://www.uniprot.org/uniprot/PSAI_THEEB PSAI_THEEB]] May help in the organization of the PsaL subunit. [[http://www.uniprot.org/uniprot/PSAB_THEEB PSAB_THEEB]] PsaA and PsaB bind P700, the primary electron donor of photosystem I (PSI), as well as the electron acceptors A0, A1 and FX. PSI is a plastocyanin/cytochrome c6-ferredoxin oxidoreductase, converting photonic excitation into a charge separation, which transfers an electron from the donor P700 chlorophyll pair to the spectroscopically characterized acceptors A0, A1, FX, FA and FB in turn. Oxidized P700 is reduced on the lumenal side of the thylakoid membrane by plastocyanin or cytochrome c6. [[http://www.uniprot.org/uniprot/PSAJ_THEEB PSAJ_THEEB]] May help in the organization of the PsaE and PsaF subunits. [[http://www.uniprot.org/uniprot/PSAA_THEEB PSAA_THEEB]] PsaA and PsaB bind P700, the primary electron donor of photosystem I (PSI), as well as the electron acceptors A0, A1 and FX. PSI is a plastocyanin/cytochrome c6-ferredoxin oxidoreductase, converting photonic excitation into a charge separation, which transfers an electron from the donor P700 chlorophyll pair to the spectroscopically characterized acceptors A0, A1, FX, FA and FB in turn. Oxidized P700 is reduced on the lumenal side of the thylakoid membrane by plastocyanin or cytochrome c6. [[http://www.uniprot.org/uniprot/PSAD_THEEB PSAD_THEEB]] PsaD can form complexes with ferredoxin and ferredoxin-oxidoreductase in photosystem I (PS I) reaction center. [[http://www.uniprot.org/uniprot/PSAE_THEEB PSAE_THEEB]] Stabilizes the interaction between PsaC and the PSI core, assists the docking of the ferredoxin to PSI and interacts with ferredoxin-NADP oxidoreductase. | + | [https://www.uniprot.org/uniprot/PSAA_THEVB PSAA_THEVB] PsaA and PsaB bind P700, the primary electron donor of photosystem I (PSI), as well as the electron acceptors A0, A1 and FX. PSI is a plastocyanin/cytochrome c6-ferredoxin oxidoreductase, converting photonic excitation into a charge separation, which transfers an electron from the donor P700 chlorophyll pair to the spectroscopically characterized acceptors A0, A1, FX, FA and FB in turn. Oxidized P700 is reduced on the lumenal side of the thylakoid membrane by plastocyanin or cytochrome c6.<ref>PMID:10066799</ref> <ref>PMID:10066800</ref> <ref>PMID:11418848</ref> <ref>PMID:8901876</ref> |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | | | |
| | ==See Also== | | ==See Also== |
| - | *[[Photosystem I|Photosystem I]] | + | *[[Photosystem I 3D structures|Photosystem I 3D structures]] |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Photosystem I]] | + | [[Category: Large Structures]] |
| - | [[Category: Thermosynechococcus elongatus]] | + | [[Category: Thermosynechococcus vestitus BP-1]] |
| - | [[Category: Adams, P D]] | + | [[Category: Adams PD]] |
| - | [[Category: Brunger, A T]] | + | [[Category: Brunger AT]] |
| - | [[Category: Fromme, P]] | + | [[Category: Fromme P]] |
| - | [[Category: Fromme, R]] | + | [[Category: Fromme R]] |
| - | [[Category: Levitt, M]] | + | [[Category: Levitt M]] |
| - | [[Category: Schroeder, G F]] | + | [[Category: Schroeder GF]] |
| - | [[Category: Chlorophyll]]
| + | |
| - | [[Category: Chromophore]]
| + | |
| - | [[Category: Electron transfer]]
| + | |
| - | [[Category: Electron transport]]
| + | |
| - | [[Category: Membrane]]
| + | |
| - | [[Category: Membrane protein]]
| + | |
| - | [[Category: Metal-binding]]
| + | |
| - | [[Category: Photosynthesis]]
| + | |
| - | [[Category: Photosystem]]
| + | |
| - | [[Category: Photosystem i]]
| + | |
| - | [[Category: Thylakoid]]
| + | |
| - | [[Category: Thylakoidmembrane]]
| + | |
| - | [[Category: Transmembrane]]
| + | |
| Structural highlights
4fe1 is a 10 chain structure with sequence from Thermosynechococcus vestitus BP-1. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
| | Method: | X-ray diffraction, Resolution 4.9228Å |
| Ligands: | , , , , , |
| Resources: | FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT |
Function
PSAA_THEVB PsaA and PsaB bind P700, the primary electron donor of photosystem I (PSI), as well as the electron acceptors A0, A1 and FX. PSI is a plastocyanin/cytochrome c6-ferredoxin oxidoreductase, converting photonic excitation into a charge separation, which transfers an electron from the donor P700 chlorophyll pair to the spectroscopically characterized acceptors A0, A1, FX, FA and FB in turn. Oxidized P700 is reduced on the lumenal side of the thylakoid membrane by plastocyanin or cytochrome c6.[1] [2] [3] [4]
Publication Abstract from PubMed
In X-ray crystallography, molecular replacement and subsequent refinement is challenging at low resolution. We compared refinement methods using synchrotron diffraction data of photosystem I at 7.4 A resolution, starting from different initial models with increasing deviations from the known high-resolution structure. Standard refinement spoiled the initial models, moving them further away from the true structure and leading to high R(free)-values. In contrast, DEN refinement improved even the most distant starting model as judged by R(free), atomic root-mean-square differences to the true structure, significance of features not included in the initial model, and connectivity of electron density. The best protocol was DEN refinement with initial segmented rigid-body refinement. For the most distant initial model, the fraction of atoms within 2 A of the true structure improved from 24% to 60%. We also found a significant correlation between R(free) values and the accuracy of the model, suggesting that R(free) is useful even at low resolution.
Improving the accuracy of macromolecular structure refinement at 7 A resolution.,Brunger AT, Adams PD, Fromme P, Fromme R, Levitt M, Schroder GF Structure. 2012 Jun 6;20(6):957-66. PMID:22681901[5]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Klukas O, Schubert WD, Jordan P, Krauss N, Fromme P, Witt HT, Saenger W. Photosystem I, an improved model of the stromal subunits PsaC, PsaD, and PsaE. J Biol Chem. 1999 Mar 12;274(11):7351-60. PMID:10066799
- ↑ Klukas O, Schubert WD, Jordan P, Krau N, Fromme P, Witt HT, Saenger W. Localization of two phylloquinones, QK and QK', in an improved electron density map of photosystem I at 4-A resolution. J Biol Chem. 1999 Mar 12;274(11):7361-7. PMID:10066800
- ↑ Jordan P, Fromme P, Witt HT, Klukas O, Saenger W, Krauss N. Three-dimensional structure of cyanobacterial photosystem I at 2.5 A resolution. Nature. 2001 Jun 21;411(6840):909-17. PMID:11418848 doi:10.1038/35082000
- ↑ Krauss N, Schubert WD, Klukas O, Fromme P, Witt HT, Saenger W. Photosystem I at 4 A resolution represents the first structural model of a joint photosynthetic reaction centre and core antenna system. Nat Struct Biol. 1996 Nov;3(11):965-73. PMID:8901876
- ↑ Brunger AT, Adams PD, Fromme P, Fromme R, Levitt M, Schroder GF. Improving the accuracy of macromolecular structure refinement at 7 A resolution. Structure. 2012 Jun 6;20(6):957-66. PMID:22681901 doi:10.1016/j.str.2012.04.020
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