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4fe1

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Revision as of 17:59, 5 August 2016

Improving the Accuracy of Macromolecular Structure Refinement at 7 A Resolution

Structural highlights

4fe1 is a 12 chain structure with sequence from Thermosynechococcus elongatus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	, , , , , ,
Related:	1jb0, 3pcq, 3lw5
Activity:	Photosystem I, with EC number 1.97.1.12
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[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). [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. [PSAI_THEEB] May help in the organization of the PsaL subunit. [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. [PSAJ_THEEB] May help in the organization of the PsaE and PsaF subunits. [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. [PSAD_THEEB] PsaD can form complexes with ferredoxin and ferredoxin-oxidoreductase in photosystem I (PS I) reaction center. [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.

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^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ 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

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 See Also
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/4fe1"

@@ Line 1: / Line 1: @@
 ==Improving the Accuracy of Macromolecular Structure Refinement at 7 A Resolution==
 <StructureSection load='4fe1' size='340' side='right' caption='[[4fe1]], [[Resolution|resolution]] 4.92&Aring;' scene=''>
@@ Line 6: / Line 7: @@
 <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='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'>[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://www.rcsb.org/pdb/explore.do?structureId=4fe1 RCSB], [http://www.ebi.ac.uk/pdbsum/4fe1 PDBsum]</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>
 == Function ==
@@ Line 18: / Line 19: @@
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 4fe1" style="background-color:#fffaf0;"></div>
 ==See Also==

4fe1

From Proteopedia

Revision as of 17:59, 5 August 2016

Improving the Accuracy of Macromolecular Structure Refinement at 7 A Resolution

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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