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3a38

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Crystal structure of high-potential iron-sulfur protein from Thermochromatium tepidum at 0.7 angstrom resolution

Structural highlights

3a38 is a 1 chain structure with sequence from Thermochromatium tepidum. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 0.7Å
Ligands:	, ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

HIP_THETI Specific class of high-redox-potential 4Fe-4S ferredoxins. Functions in anaerobic electron transport in most purple and in some other photosynthetic bacteria and in at least one genus (Paracoccus) of halophilic, denitrifying bacteria.

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

Publication Abstract from PubMed

The positions of hydrogen atoms significantly define protein functions. However, such information from protein crystals is easily disturbed by X-rays. The damage can not be prevented completely even in the data collection at cryogenic temperatures. Therefore, the influence of X-rays should be precisely estimated in order to derive meaningful information from the crystallographic results. Diffraction data from a single crystal of the high-potential iron-sulfur protein (HiPIP) from Thermochromatium tepidum were collected at an undulator beamline of a third generation synchrotron facility, and were merged into three data sets according to X-ray dose. A series of structures analyzed at 0.70A shows detailed views of the X-ray induced perturbation, such as the positional changes of hydrogen atoms of a water molecule. Based on the results, we successfully collected a low perturbation data set using attenuated X-rays. There was no influence on the crystallographic statistics, such as the relative B factors, during the course of data collection. The electron densities for hydrogen atoms were more clear despite the slightly lower resolution.

Detailed assessment of X-ray induced structural perturbation in a crystalline state protein.,Takeda K, Kusumoto K, Hirano Y, Miki K J Struct Biol. 2010 Feb;169(2):135-44. Epub 2009 Sep 24. PMID:19782139^[1]

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

References

↑ Takeda K, Kusumoto K, Hirano Y, Miki K. Detailed assessment of X-ray induced structural perturbation in a crystalline state protein. J Struct Biol. 2010 Feb;169(2):135-44. Epub 2009 Sep 24. PMID:19782139 doi:10.1016/j.jsb.2009.09.012

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/3a38"

@@ Line 1: / Line 1: @@
 ==Crystal structure of high-potential iron-sulfur protein from Thermochromatium tepidum at 0.7 angstrom resolution==
-<StructureSection load='3a38' size='340' side='right' caption='[[3a38]], [[Resolution|resolution]] 0.70&Aring;' scene=''>
+<StructureSection load='3a38' size='340' side='right'caption='[[3a38]], [[Resolution|resolution]] 0.70&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3a38]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermochromatium_tepidum Thermochromatium tepidum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3A38 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3A38 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3a38]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermochromatium_tepidum Thermochromatium tepidum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3A38 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3A38 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 0.7&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3a39|3a39]], [[1iua|1iua]], [[1eyt|1eyt]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></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=3a38 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3a38 OCA], [http://pdbe.org/3a38 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3a38 RCSB], [http://www.ebi.ac.uk/pdbsum/3a38 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3a38 ProSAT]</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=3a38 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3a38 OCA], [https://pdbe.org/3a38 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3a38 RCSB], [https://www.ebi.ac.uk/pdbsum/3a38 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3a38 ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/HIP_THETI HIP_THETI]] Specific class of high-redox-potential 4Fe-4S ferredoxins. Functions in anaerobic electron transport in most purple and in some other photosynthetic bacteria and in at least one genus (Paracoccus) of halophilic, denitrifying bacteria.
+[https://www.uniprot.org/uniprot/HIP_THETI HIP_THETI] Specific class of high-redox-potential 4Fe-4S ferredoxins. Functions in anaerobic electron transport in most purple and in some other photosynthetic bacteria and in at least one genus (Paracoccus) of halophilic, denitrifying bacteria.
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 33: / Line 33: @@
 __TOC__
 </StructureSection>
+[[Category: Large Structures]]
 [[Category: Thermochromatium tepidum]]
-[[Category: Hirano, Y]]
+[[Category: Hirano Y]]
-[[Category: Kusumoto, K]]
+[[Category: Kusumoto K]]
-[[Category: Miki, K]]
+[[Category: Miki K]]
-[[Category: Takeda, K]]
+[[Category: Takeda K]]
-[[Category: Electron transport]]
-[[Category: Iron]]
-[[Category: Iron-sulfur]]
-[[Category: Iron-sulfur cluster]]
-[[Category: Metal-binding]]
-[[Category: Transport]]

3a38

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Crystal structure of high-potential iron-sulfur protein from Thermochromatium tepidum at 0.7 angstrom resolution

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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