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1dfd

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OXIDISED DESULFOVIBRIO AFRICANUS FERREDOXIN I, NMR, 19 STRUCTURES

Structural highlights

1dfd is a 1 chain structure with sequence from Desulfocurvibacter africanus. Full experimental information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	Solution NMR
Ligands:
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

FER1_DESAF Ferredoxins are iron-sulfur proteins that transfer electrons in a wide variety of metabolic reactions.

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 solution structure of the 64 amino acid Fe4S4 ferredoxin I from Desulfovibrio africanus has been determined using two-dimensional 1H NMR spectroscopy. Sequence-specific assignments were obtained for 59 amino acid residues and the structure determined with the program DIANA on the basis of 549 nuclear Overhauser enhancement (NOE) upper distance limits, and four dihedral angle and 52 distance constraints for the Fe4S4 cluster. The NMR structure was refined using the simulated annealing and energy minimisation protocols of the program X-PLOR to yield a final family of 19 structures selected on the basis of good covalent geometry and minimal restraint violations. The r.m.s.d. values to the average structure for this family are 0.49(+/-0.07) A and 0.94(+/-0.09) A for the backbone and heavy-atoms of residues 3 to 62, respectively.The NMR structure has been compared to the previously reported X-ray structures for the two molecules within the asymmetric unit of the crystal, which have a network of seven hydrogen bonds between them. This intermolecular interface, involving residues 38, 40 to 43 and 46, has the same conformation in the solution structures showing that the crystal packing does not perturb the structure. There are three regions in which the NMR and X-ray structures differ: around the cluster, a turn involving residues 8 to 10, and a loop involving residues 29 to 32. In the family of solution structures the backbone of the loop region incorporating residues 29 to 32 is well-defined whilst in both of the X-ray molecules it is ill-defined. The small differences between the X-ray and NMR structures for the cluster environment and the turn between residues 8 to 10 probably reflects a lack of NMR constraints. The observation of relatively rapid amide NH hydrogen exchange of NH groups close to the cluster, together with rapid flipping for Phe25, which is also close to the cluster, indicates that the cluster environment is more dynamic than the corresponding regions of related Fe/S proteins.

Determination of the structure of oxidised Desulfovibrio africanus ferredoxin I by 1H NMR spectroscopy and comparison of its solution structure with its crystal structure.,Davy SL, Osborne MJ, Moore GR J Mol Biol. 1998 Apr 3;277(3):683-706. PMID:9533888^[1]

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

References

↑ Davy SL, Osborne MJ, Moore GR. Determination of the structure of oxidised Desulfovibrio africanus ferredoxin I by 1H NMR spectroscopy and comparison of its solution structure with its crystal structure. J Mol Biol. 1998 Apr 3;277(3):683-706. PMID:9533888 doi:S0022-2836(98)91631-X

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1dfd"

Categories: Desulfocurvibacter africanus | Large Structures | Davy SL | Moore GR | Osborne MJ

@@ Line 1: / Line 1: @@
 ==OXIDISED DESULFOVIBRIO AFRICANUS FERREDOXIN I, NMR, 19 STRUCTURES==
-<StructureSection load='1dfd' size='340' side='right' caption='[[1dfd]], [[NMR_Ensembles_of_Models | 19 NMR models]]' scene=''>
+<StructureSection load='1dfd' size='340' side='right'caption='[[1dfd]]' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1dfd]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Desulfovibrio_africanus Desulfovibrio africanus]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DFD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1DFD FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1dfd]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Desulfocurvibacter_africanus Desulfocurvibacter africanus]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DFD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1DFD FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><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">Solution NMR</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=1dfd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dfd OCA], [http://pdbe.org/1dfd PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1dfd RCSB], [http://www.ebi.ac.uk/pdbsum/1dfd PDBsum]</span></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</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=1dfd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dfd OCA], [https://pdbe.org/1dfd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1dfd RCSB], [https://www.ebi.ac.uk/pdbsum/1dfd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1dfd ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/FER1_DESAF FER1_DESAF]] Ferredoxins are iron-sulfur proteins that transfer electrons in a wide variety of metabolic reactions.
+[https://www.uniprot.org/uniprot/FER1_DESAF FER1_DESAF] Ferredoxins are iron-sulfur proteins that transfer electrons in a wide variety of metabolic reactions.
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
 Check<jmol>
   <jmolCheckbox>
-    <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/df/1dfd_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/df/1dfd_consurf.spt"</scriptWhenChecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
   </jmolCheckbox>
-</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/main_output.php?pdb_ID=1dfd ConSurf].
 <div style="clear:both"></div>
 <div style="background-color:#fffaf0;">
@@ Line 29: / Line 31: @@
 ==See Also==
-*[[Ferredoxin|Ferredoxin]]
+*[[Ferredoxin 3D structures|Ferredoxin 3D structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Desulfovibrio africanus]]
+[[Category: Desulfocurvibacter africanus]]
-[[Category: Davy, S L]]
+[[Category: Large Structures]]
-[[Category: Moore, G R]]
+[[Category: Davy SL]]
-[[Category: Osborne, M J]]
+[[Category: Moore GR]]
-[[Category: 4fe-4s cluster]]
+[[Category: Osborne MJ]]
-[[Category: Electron transport]]
-[[Category: Electron-transfer protein]]
-[[Category: Oxidised desulfovibrio africanus ferredoxin i]]

1dfd

From Proteopedia

Current revision

OXIDISED DESULFOVIBRIO AFRICANUS FERREDOXIN I, NMR, 19 STRUCTURES

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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