4fe1

From Proteopedia

(Difference between revisions)

Current revision

Improving the Accuracy of Macromolecular Structure Refinement at 7 A Resolution

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.

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

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 4: / Line 4: @@
 == Structural highlights ==
 <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" 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>, <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]] 4.9228&#8491;</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='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>
 </table>
@@ Line 20: / Line 21: @@
 ==See Also==
-*[[Photosystem I|Photosystem I]]
+*[[Photosystem I 3D structures|Photosystem I 3D structures]]
 == References ==
 <references/>

4fe1

From Proteopedia

Current revision

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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